Chris told me he was using Megasquirt 3 inside a 2 box. Really don't know for sure and I haven't looked to see it the 3 has been approved by NHRA as of yet. Thus the reason he wanted to borrow our NHRA approved AEM in 2010. I would just stick with whats been proven and works.
Jeff Taylor has been very successful with both Bigstuff3 and FAST. We prefer tuning with AEM or FAST.