If 2 different ECU's giving similar problems, it can be more to do with wiring than anything else, especially if you need to hold it up for it to work. ECU inside is solid circuits, so should not make any difference what position it is on. If it idles at 2k its probably overfuelling, hence pops from exhaust, which might be mistaken with misfire. Also - Supra normally idles high when cold. Have you checked temperature sensor - one which feeds back to ECU? Is it still idle at 2k rpms when hot? Have you done pin test to pull out fault codes?
I've got NA auto and NA manual ECU's here, both were working fine, only took them out when I was doing engine swaps to TT and later to V8.