Did everyone miss where he said it backfires? Backfire sounds like it is missing, for it to miss it sounds almost certianly like an ignition issue, old shagged coilpacks almost always cause a miss around peak torque (4500-5500rpm). There are loads of threads about this issue, surely this has to be the problem?
Check the spark plug gap as well, 0.8 is the largest I would go. Toshi is in Japan, most japs tune the cars very rich around 10:1 from what I've seen, this exaggerates any weak spark problems massively making any misses due to poor spark even worse, you don't have to see cracks/etc for the coils to be stuffed, mine looked perfect and were stuffed, fixing the tune up from 10:1 to 12:1 completely removed the misfire in my situation as well.
The only other thing I would bet money on is the intake sucking shut, but I can't see how this would cause a misfire.
edit: You say you have an R33 ecu but these cannot be nistuned, the most likely option is an R32 ecu, however these can't control VCT, how is your VCT being controlled? If it isn't switching off at 5000rpm correctly and is keeping the exhaust cam retarded you will see a big dip in power over 5000rpm, make sure the VCT is switching on and off correctly at the right rpm, this could also be your issue, I can't see it would cause any backfires though.
edit2: just saw that it wasn't nistuned, ignore my first edit.