Ok a couple of things, first check the timing is good, sounds like it may be out 1-2 on the exhaust or intake timing. Then check that the VVT solenoid has been wired up, this is often not wired up, it is probably not causing this issue but check it anyway, its 12v live is also shared with the idle control valve and the o2 heater, should show 12v live with ign on ground it against the car. Check the gap on your plugs and for any cracks in the packs.
Also check that the block has been modified to suit the r33 exhaust manifold, if you have not done this then the head will not sit flush on the block and it may show symptoms like this.
and then lastly switch the ECU over into diagnostic mode and check to see if it spits back any error codes. Should show code 55 for all sensors OK. Then probably wouldn't harm to go to mode 2 or whatever it is and check the afr's when it breaks down.
The led is on for lean off for rich, if its stays on either of these when breaking down then check your fuel system accordingly. Thats for single led ECU's
Edit: wait a minute your not still using the stock vl fuel pump are you?