My last project was a 2.8L inline 6 using an EDIS-6 coil and made 540whp on pump at 22psi of boost with 0.035 plug gap, no problem. I think the edis-6 is good for around 750whp. Two edis-4 modules (edis-8) should be good for around 1000whp.
The edis coils are excellent.
First problem:
Take that MSD and throw it in the garbage.
Drive the EDIS coil directly with VEMS. 3.8ms under full load is about right.
Second problem:
If you still have issues, throw aways the "screamin demon" coils and get OEMs ones.
Seriously, this will work.