Can the MSD ignition box be used with a stock coil as that would make it simpler?
If you are using the stock amp with an after market coil then it won't be helping matters. Even with a new OEM amp it remains the weak link in the chain when you want to run the type of plug gaps used by modern cars with >400hp.
A better amp can and has been used with the stock coil, if that's the case then it would be best to keep the plug gap stock. It's a bit like running a big amp with small speakers, it will work fine until you turn the volume up and it'll blow your speakers.
I'd recommend if your coil is already in situ then leave it and get the amp in as well, run your 0.9mm gaps and enjoy smoother low load running.
Alternatively, leave it as it is and run 0.6mm gaps and forget about it.
0.9mm gaps with a standard amp on a larger after market coil is probably the most difficult combination.
Whatever path you choose use OEM leads. This is not a throw away comment but from my own back to back tests.