If it started running poorly as soon as you put the repaired ECM in, then I'd say the ECM is the problem. I have tried to fix some of my ECMs and if you don't get certain things fixed, or fixed right, then it will run like crap. Sometimes there are things wrong with an ECM that is hard to find and fix.
What I would do, is try to borrow a known good ECM (or try your ECM in another 90-95 samurai) and see if a different ECM fixes the running issue (or see if the poor running follows your ECM to the other samurai).
Who fixed your ECM? Is there any type of warranty that came with the repair?