The least restrictive would be w/rjc's 5/4" d/p. But a 3.0" or 3.5" would serve you just as well w/an external w/g, not requiring any mod's to the size of the bi-pass port for boost control.
You really needed to post more info on your mod's.
If the flange i.d. is too small, you can purchase another flange w/the correct i.d. and have it welded on or consider new. 3" should be sufficient. I ran a 71gtq w/ext. w/g and 3" dia. w/600+ to the wheels. No problem.