Very interesting discussion indeed.

For some reason, I personally like the hardware on the earlier engine more. Maybe because they REV higher, and also they have more "meat" around cylinders making them in my eyes superior as a base to start with. I was not aware that the cam is variable on the .98 models as well so that's a very good find for me.

What I don't like about this engine is the rod ratio and the fuel injection part.
Rod ratio in M104.980 is 1,81. It's little better on 3,2 and 3,4 liter engine that has the same stoke 84mm and same length rods (145mm). Now the 3.6 L engine has rods from M104 2,8 that are 144mm right, making the rod ratio 1.56

Copy:
Typically, an engine with a higher rod ratio will produce a little more power from mid-range to peak RPM. Longer rods require the wrist pin to be located higher in the piston, or the engine has to have a taller deck height to accommodate longer rods. Longer rods also mean shorter and lighter pistons can be used, so the additional weight of the rods is more or less offset by the reduced weight of the pistons.

One of the disadvantages of longer rods and a higher rod ratio is that low RPM intake vacuum is reduced somewhat. Reduced air velocity into the engine hurts low-speed throttle response and torque, which is not good for everyday driving or street performance but works well on a high-revving race engine.

I wonder if there is anyone who has gone from CIS to fuel injected system and done 1:1 comparison how much is really hidden there and how much is really hidden in the intake manifold. If you look at the design on CIS intake manifold it has quite long runners that do not indicate it is a high revving engine but as always with OEM, they had to compromise many things for the sake of performance when they designed this engine.

Does the newer engine intake manifold bolts to M104.98 engines is the intake flange same and are the intake bolts on same location?