390's can be found some what cheap so if the motor is original to the car then I'd find another 390 off the craigslist to build & store the original motor. The 360/390/410 all share the same block with different internals, the 360 has a 352 crank with 390 rods & 360/390 4V pistons (same thing), 410 has a 428 crank with 390 rods & 410 pistons (some truck 390's had 410 pistons installed from the factory with the 390 crank ending up with a 8:1 CR).
The exhaust is really restrictive on the FE Mustangs along with the top end. A aluminum RPM performer intake is a must with a FE (not just for power but for the weight loss on the front end), as for the heads the only good set of stock heads are CJ's & C6AE-R heads (these need CJ sized valves installed) but other than that I'd go with aluminum.
As for stroking the motor I'm going with a 445 stroker kit for my 390, bolts right in the block with no machine work needed (I'd still have it internally balanced though).
If you're wanting to build a FE then I'd go to SurvivalMotorSports.com, Barry is considered a FE guru.