BEWARE cooling/overheating problems in W124 V8's. If overheated badly even once, the valvetrain is toast. Perhaps THE best indicator of engine condition (short of a detailed inspection by a pro) is to open up the oil-cap and peer inside. The cams and valves should look shinny, metallic, mirror like. If it is black, gummy, etc then walk away.
From what I've read and been told the 92's were quicker than the late 93 and on cars. If both in question were 92's then my next question would be...did the slow car have ASR? I have driven many many W124 V8's over the years. The 4.2's that have ASR are simply slower, even if you don't hit ASR. I will defer to Benzmac or MB DOC (he must have a PhD!) to explain exactly why. All US 400E's and E420's had a 2.24:1 rear diff. Euro bound 400E's shared the 2.65 with the E320 cars. (so I'm told, have yet to drive a euro 400E) ALL 4.2 M119 W124's need more rubber to perform their best. Better tires equal better performance.
You mentioned the slow car just had a tune-up. I have heard that MB engines do not always like platinum spark plugs. Since most of a tuneup (on that engine) is changing the plugs that could be a cause. In driving W124's many are the same in appearance and other standard characteristics. Each of them drives a little differently though. Think of it as each car's "personality". Its hard to describe but the combination of maintenance, ambient temp, road conditions, tires fitted, etc can make each car feel unique.
One thing it could be is "feel". The 400E's had a MONSTER flat spot between the gears where the tranny would not downshift into 1st past 25mph. If you hit the gas at 30mph all you get is 2700rpm in 2nd gear (which is like 3rd on most cars) and not much thrust. Hit the gas at 20-25 and you are thrust back into the seat on a big 4th-1st downshift. 2nd gear acceleration does not get good until you kick it down at about 60-65mph. Shift manually, it will make engine differences more evident. Little things like that can make one car feel weaker than another. BTW The tranny is designed to function that way. Benzmac tells me there is a tweak for it....
Of course the biggest power change factor of those cars is temperature. As the engine gets over 100 C it loses much HP's. Outside temp hurts its performance as well. Engine at 105 C in traffic on a 95 degree day...you will get 6-cyl performance. Engine at 80 C on a 40 degree night...runs like a raped ape.
Even on a good night a Grand National would probably take them in a straight line. The acceleration curve is similar...wait for the car to get up on its cams or boost then the real acceleration starts. Of course, the one I am familiar with has a Benzmac co-built engine, various other mods, racing slicks, 2-stage alchohol injection system, etc. Dunno, we may have to sick the 500E on the GN. j/k (Jeff are you reading this?!)
Keep us posted on how things go, we would be happy to answer any pre-purch questions you might have. I still recommend you get it inspected by a local professional. Best of luck in your search.