Alright, let's throw down some information.
Where to start...
Heads:
Alright. There were two (count'em) and only two separate types of cylinder heads.
There is the round port "late" style head which came on the HFM and LH managed engines. This head can be easily seen by the fact that the water outlet is on the front of the engine. It comes out, make a 90 degree turn, and runs into the top of the water pump. This head is found on any 2.8/3.2 engine (any in the 89.9mm bore class) and any of it's Hi-po Variants (3.6AMG, The EFI brabus and carlsson, etc.) This head had a slider on the intake side as opposed to an idler sprocket on the earlier heads.
The oval port head is (as far as I know) only on CIS equipped cars. CIS = Oval port and oval port = cis. Someone said they knew of an EFI Oval port head, but I've never actually seen it in any country, nor is it referred to in any MB literature. This head is easy to spot because it's CIS, and the water outlet is on the side of the head, in the same spot an M103 water outlet is, right in front of cylinder 1 Intake. This head is only found on the 3.0 CIS M104 and its variants. AKA the early 3.4 AMG motors that are CIS as well as the early brabus -24v motors that found their way into the Brabus 190e 24valve cars. These engines had a idler sprocket on the head, right below the intake cam instead of the slider on the later engines. Any engine that was based on an 88.5mm bore block had this head.
Either Cylinder head could come with a distributor on the exhaust camshaft. This is dependent on fueling. CIS and LH injected engines had dizzys on the exhaust. HFM/Motronic motors did not. Both heads have a 48mm combustion chamber. Mine were measured on earlier heads, and max huges said his head off of a 1997 W210 came in also at 48cc's.
Camshaft adjuster. ALL M104's had camshaft adjusters on the intake camshaft. 104.98 engines advanced the camshaft 34 degrees on activation and the .99/.94 engines advanced it 32 degrees. The USA CIS engines produced after 4/1991 only advanced the engine 29 degrees. IIRC the turn on for the cam was 1000rpm (Per FSM, but I believe it was actually 1400rpm) and the shut off was 5k for CIS motors and 4800 on the .99's.
Valvetrain:
AFAIK all the engines that MB produced that came in a production car (I.e. non aftermarket tuner) came with a 35mm intake valve and a 31mm exhaust valve.
The intake valve only came in two stem sizes, 8mm and 7mm. Only the very early CIS engines had the 8mm intake valve. All other engines were 7mm valve stems. Any Cis engine with the engine serial before 12-017952 has the 8mm valve. All other motors are 7mm valves.
The exhaust valve came in 7,8, and 9mm variants. Only the CIS motors again came with a 9mm variant. The 9mm valves only came on the 8mm intake motors, while the 7mm intake valves were either 7mm or 8mm on the exhaust valve.
The early M104.99x motors had an 8mm valve up until engine number 12-042686 and the .98x motors had an 8mm stem for the engines 12-017953 To 12-042363. Is your engine serial past this? 7mm exhaust valve. All .94x engines should be 7mm/7mm.
Valve guides were either brass or sintered iron. I cant find a production breakpoint for the change, but all engines with valves of two different stem sizes and only the very early 7mm/7mm engines were brass valve guides. I'd say if your engine was build in 1994+ it's a safe bet that it's a sintered iron guide.
Retainers: There were two groups of retainers used: the single groove, and the triple groove. The early CIS motors, before the 7mm/7mm engines (before 12-042363) should have a single groove retainer. After 12-042364 on the .98 and before 12-060026 on the .99 and before 12-021699 on the .94 engines are triple groove retainers. After that on the .94 and .99 engines are single groove retainers again.
Valve springs: I've seen two arrangements for valve springs, an beehive spring and a double spring with an outer and an inner spring. Each of these has separate spring seats, but the seats are removable and can be transferred to any engine with the same size valve stem (i.e. you can put the springs and seats from a 7/7 engine on another 7/7 engine but not an engine that's 8mm/9mm). I believe mid to late 1993 3.2's only had the outer valve spring as opposed to the double as I've seen an engine come apart like that, but MB does not list it in the FSM. On 11/1993, all engines produced after it have a conical valve spring and the valve hat/spring retainer/whatever you want to call it is not interchangeable with the earlier single/dual valve springs.
Cams: Aside from the AMG's there were 2 basic intake and 2 basic exhaust cams provided. The AMG Model does have a different intake cam. If anyone has the info on that, let me know.
http://www.w124performance.com/service/w124CD1/Program/Engine/104/05-2210.pdf
The camshafts do not have separate thrust bearings like the M102/M103 engines, except for the very early M104.98x engines which do. I believe this corresponds to the 8mm/9mm valve engines, but I cannot confirm this. Either way, they are very early engines.
The early M104's have centering pins on each of the camshaft caps, however these were done away with on 1/93 production date, and past that the cam caps self centered on the cams.
All M104's had hydraulic lash adjusters and are cam on bucket type valve actuation. The diameter of these actuators is 35mm.
Valve covers: There appear to be two separate valve covers, and again it's fuel injection dependent. CIS and LH engines had the flat cover with MERCEDES-BENZ written down the front while the later style engines with HFM/Motronic had a more angular cover with the intake pipe running over the top and two breathers over the top of cylinder 5/6. These have separate front cam cover types and the flat-type cam sprocket covers cannot be used with the angular valve cover specific cam sprocket covers.
THE BLOCK:
All M104 blocks have a deck height of 217.625mm and have the crankshaft offset from the bore center-line 1mm towards the intake side.
Alright, there are two major break points for the blocks. One is for the CIS .98 engines which has a big 10 cast into the side and an 88.5 mm bore and the other is for the .94/.99 series of engines that starts with an 89.9mm bore and is easy to tell because it has significantly more ribbing running the length of the block near the crankshaft area.
All the blocks have windows directly above the crankshaft. Since 1/1991, additional windows were placed in the block directly adjacent to the crank main cap bosses between them and the exterior of the block.
After that, in 4/1991 the additional ribs were placed down the sides of the block. This occured with the introduction of the M104.990 engines in the New W140 chassis. As a result there are three different Knock sensor control modules, so match yours up with the block you have, or the block you plan on using. The vast majority of you will just have the 3rd type of knock sensor.
Note: the LH injected .99 engines did not have the 4 bolt bosses on the intake side of the block so that the lower intake manifold of the HFM cars could bolt to it. Thus you cannot use an LH block on an HFM car unless you plan on changing the lower intake manifold or plan on using your own setup. Vise-versa (HFM block on LH) is fine however.
Oil squirters: Oil squirters were provided on all engines built before 1/1994. They have check valves in them and a spring that does not allow the oil squirters to function below a certain oil pressure (not stated in FSM) so that the engine is not oil starved at idle.
Crankshafts:
All crankshafts have a 58mm main journal diameter (nominal) and the thrust bearing is located on journal 5, between cylinders 4 and 5.
In the M104, 4 different crankshafts came in vehicles sold through MB (I cant vouch for aftermarket tuners)
The M104.98 engines used an M103 crank. All M103 cranks and the M104.98 cranks are the same at 80.25mm bore and 48lbs bare (no timing sprocket)
The M104.99 engines us a crank that's derived from the OM603 engines at 84mm of stroke. The weight on these cranks is 49lbs and you can see it's diesel heritage as it has counterweights that are much wider than the .98 counterweights, though they're just as thin which is why it's only a pound heavier. The 3.4L AMG engines appear to use this crankshaft and the 91mm bore.
The M104.94 engines used a 73.5mm stroke crankshaft that was specific to the 2.8L engine. I didn't have one of these cranks available to me at the time of weighing
The 3.6L AMG engine uses the 92.4mm stroke crank of the 350SD as it's basis and is radically lightened and there are grooves on the inside of each counterweight to clearance the piston on the way down. For reference the 350SD crank weighs in at a staggering 67lbs.
The numbers should be laser etched on the snout of the crank, but i've seen multiple early cranks that were not laser etched.
To the best of my knowledge all of the cranks were forged, but I have not seen a crank made after 1995 so I cannot confirm that's true or not. All have been induction hardened at the load bearing surfaces.
Connecting rods:
All engines to the best of my knowledge use a 1.998 (48mm "honda") sized main bearing with a 22mm big end width and a 22mm wrist pin. All M104's use the piston guided rods, where the piston stabilizes the lateral movement of the rod, not the crankshaft. The crankshafts are 48mm in width.
The 3.2 and 3.0 engines use a 145mm length rod. This is the same rod used in the 2.3 M102 (maybe others) as well as the 2.6 and 3.0 M103's.
The 2.8 uses a proprietary 149mm rod.
The 3.6 I'm not sure of but I believe it uses a derivative of the M111 144mm rods.
Pistons: all M104's came with cast pistons. All the engines I've seen used Mahle pistons with an antifriction coating on the skirts, but I believe Kolbenschmitt was also OEM for M104's. As for piston sizes, I'm not perfectly sure yet. I hope to have some dish/pop up information soon.
All .98 engines started at 88.5mm same as the M103.98's while the .99/.94 engines are bored to 89.9mm. The C36 engine I believe starts life at 91mm.
Oil pumps: The M104's came with a spur-gear type oil pump that's chain driven off the cam. The M104 pump is similar to the M103 pump but not the same, and it is driven faster than the M103 pump due to greater oil requirement in the head. There are two different width pumps in the M104 and for the life of me I cant remember what I measured the spur gear widths at. I'll get back to everyone on that too.
Windage Trays: All M104's come equipped with windage trays. Early M104's have a windage tray that goes all the way up to the oil pump, covering all six crank throws while later M104's only cover 2-6. Again, I couldn't find any info on when the switch over was.
Fuel Injection: There were 3 basic types of fuel injection. CIS, HFM, and LH
CIS is a CIS 5 injection which is not the same as the M103 setup. It gives knock control as well as the camshaft advance. It does however use an EZL and still has an exhaust cam driven dizzy. CIS scares me and I don't have much info on it.
LH came on the early W140 M104 .99's. It too has an exhaust cam driven dizzy and an EZL but uses LH injection EFI similar to that of the LH in the M119's. These engines also have aluminum intakes like the CIS but are build on a round-port -99 engine.
HFM occurs on all cars after this and has the black plastic two piece intake that you hear so much about. It's actually pretty strong, and unless you backfire through the motor repeatedly, I don't think it has a problem with boost either. I believe in 1996, the flexplate on these engines went from the 3 tab of the CIS/LH cars to a standard motronic 60-2 wheel.
I think that's all I have time for today, back to the grind...