You said that the problem was with the air in the fuel line, originating at the carb end... It could be that you overheated the engine/carb, that happens to me, I run the NTC3 as well. When the carburator overheats, it's a bitch to crank up the engine up. Maybe check out the tuning? I would also try checking the pressure line (the one that goes from the tank to the pipe); it's recommended to run a long pressure line on the NTC3, but NOT TOO LONG; try running a shorter pressure line and see if it solves the problem.
Apart from the normal problems on the car, how bout the condition of the engine? Ever tried running the engine in another car to troubleshoot? Just in case the problem lies withing the engine.
Keep us posted!