New engine won't stop stalling....

I have a 2005 rx-8, we recently put a remanufactured engine in the car, replaced the oil injectors, motor mounts, got bhr coils, after installing the engine it kept dying at idle, we searched the forums and did the resetting of the ecu - break peddle 20 times in 8 seconds, the button on the odometer and unplugged the negative battery terminal for 10 minutes etc. And it will run fine for a time, but then seems to go back to dying at every red light at idle, I have recently replaced the starter and the fuel pump as well.

Modifications to engine/tranny: k&n typhoon intake, bhr ultra lightweight flywheel, bhr coils, agency power exhaust, unorthodox pulleys.

Any help would be greatly appreciated.