There aren't many ways to get the ECU tuned. JWT sells a chip, but they run the car pretty rich to be on the safe side. You can use any piggyback system if you have enough knowledge to wire anything up. My personal choice, however, would be Nistune. You can have them load up a stock 88T tune and work from there. That said, the stock ECU will be good until you get all the basic modifications done anyway, so I'd put this lower on the priority list.
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The 88T came with the R30A. As for how much power they are rated for, I have no clue. I can't recall anybody breaking one from having too much power. There's one guy running 9s on this transmission. Anyway, the axle studs will break long before the transmission.The NA 5 speeds are good for 500hp it seems. The 84-86T transmissions are good for about 300hp from what I've seen. And the automatics are good for making cool coffee tables.