The 390 will fit, but if being installed in a car that has the reinforced shock towers, the exhaust manifolds will hit these plates. The 390 for these cars had different bolt holes in the heads for the Mustang and Cougar. I my self have re-drilled and tapped for the correct manifolds.
You need a set of 390Gt exhaust manifolds for a pattern, then you will see which holes need to be drilled and tapped, this can be done with heads installed, and engine removed. You might be able to use the gaskets for a pattern if you can find them for a Mustang 390 GT, maybe Ford motorsport. Look at this. http://www.summitracing.com/parts/SUM-111434/?rtype=10
You can probably do it with a hand drill - I have taped out plenty of things over the years. Some things to keep in mind - the depth it needs to be if it's not a through hole - which would be best done with a flat bottom tap rather than a cone tipped one. Mark depth on bit with a piece of tape for reference. Work in increments for drilling it out. Center punch every hole, start with a smaller bit to give you a guide hole/oil hole - then work your way up. Use plenty of cutting oil and be sure to know what size/index bits to use for the final size before you tap it. Also double check the tap for thread pitch you will be using - I always hold it up to the bolt to be sure they mesh evenly for a sanity check. WHen you tap it always work slowly and back the tap out every few turns to clear the chips from your threads - our use grease to hold the chips. Slow and steady wins the race!
I've seen it done. It was a guy who had a website called My Stupid 390 ougar or something like that. He basically had a junk 390 powered Galaxie and a 289 Cougar and made it work. There was beer and a torch involved.