running the MSD 6-Hemi ?

Well the engine is going to be far from stock. I am building a stock suspension 10.5 tire car, not planning to be competitive in the class but just using it as a base. I am planning to make 650hp to the wheels using a pro-charger. I am expecting dyno time to tune and with this engine a stock tune probably won't help. Have been talking with an engine builder and I am sure the engine will see the engine dyno before I put it in the car, then a chassis dyno. I am far from the engine being built but I need to decide what engine I want to use. My 340 with the B1/BA heads I have sitting under the work bench or a New style Hemi. I know either is getting injected and a pro-charger.

Will the Mega squirt control the timing and fuel, or just the fuel side? I am planning to start a build thread soon. I have been taking pics of the car as I have started taking it apart. I bought it as a roller and built a hi comp 340 with stock heads and raced it a few years. I will tell the whole story in my build thread. Thanks for all the info you guys are sharing with me as it is helping with my decision.

Trevor