the early trannys had lower 5th gear which helps a tad with larger tires. most will argue it isnt noticeable. the carriers went from 4 pin to 2 i think in 90, which is also the year they started installing EFI.
personally, i would not drive a sami unless it was EFI. it is dirt cheap to replace/ rebuild the ECMs IF they go out. they are not BAD about it...
i have had 4 EFI samis and they were all less trouble than any of the carb'd models i have owned. the carbs are finicky, and up until recently the the most popular upgrade for the carb was the weber, which has its quirks itself. samuraiguy.com is offering a 4 carb setup that is said to be able to run at any angle and give major power gains...
that wouldnt be too bad, but IMO, you can not beat EFI...