The flanges are setup nearly identical to the factory flanges. The injectors end up being about 1/8" closer to the intake valves because of the difference in flange thickness. The clearance problem I had was with the fuel injector rail. My runners were too upright and the rail would not go back on. My next runners are going to be canted towards the supercharger to get around this. I'm aiming for the runners and plenum volume to equal 3.2 liters. I should have some results posted by next weekend.