I'm running MS2, It does the job well and I have no complaints. As for the intercooler, some guys have "clocked" the trottlebody to match the stock one so you can retain your intercooler. Either way involves Fabrication so choose your battle ( I have been kicking around the idea of building a larger intercooler). If I remember correctly the MS2 (with boost control), harnesses and relay board came in around $750. I grafted a mustang TPS onto the Carrera throttlebody and used GM IAT and Coolant sensors as the MS is defaulted to read those sensors. I also went with EDIS6 which will require either buying the clewett crank trigger stuff or fabricating your own. The MS2 is defaulted to accept EDIS input and the cool thing is one "brain" will control 2 coil packs if you go twin plug..
The new MS3 is sequential but involves more wiring and set-up.
ok so what version of mega squirt should I get and how much will it cost? I already have a 3.2 intake So I will also need to make an intercooler. I really like the one you made not the first one but the one you have now.