Think it doesn't really make any difference. If GoneAgain and me compare cars, there are little detail differences between 88 and 91. (sunroof switch, keys,some small plastic bits under the bonnet that are different)
With the cars being hand-built, I think the chances of "production-errors" are smaller than the modern cars. Recalls etc are the order of the day nowadays, simply because testing etc is reduced where it should be doubled. The E34 is generally VERY well built and I can't readily think of any major improvements the model has made over the years apart from the cosmetic ones.
The early cars have solid brake rotors on the rear, I believe 90> got the vented ones. Like you would ever feel the difference

Untill production 91, the cars have V-belts instead of multi-drivebelts for the AC,PAS and other items. Not much of a shock either.
On the 3.8 issue , I agree its a "better" useable engine and not even more stressed than the S36. Many people seem to think the opposite. I dislike the fact that the bearings get shot every once in a while, the EDC keeps you awake at night and the coils etc cause problems. 3.6 has enough problems on its own, but still, itts not like I am eagerly waiting for the day I can afford an S38..Its all about low-down torque on what the 3.8 holds the title, but I don't really care that much about that. I like the way my car performs now and even if you get a 3.8 there will still be a lot of cars around that are faster.
I do believe that the early cars ( 3.6) are usually with a higher spec than the 3.8. Most 3.8's have the alcantara and regular A/C, whereas lots of 3.6s sport leather and have more options installed. This might just be in my mind, but still.
'88,'89,'90 or '91 doesn't really matter in my opinion, not even value-wise. You should concentrate on other aspects whilst looking for an M5
cheers
W