What you do to your car, all original or modified, is totally up to you. I don't own a museum so I chose to modify my '64 Hardtop with the 390. My goal was basically the same as you stated in post 1; I wanted just a bit more performance, yet smooth idle and good economy. I also wanted it to last at least 250,000 miles, like a modern engine. It took a bit of research, experimentation and cash, but I think I have a pretty good combo.
I had the engine completely rebuilt. After 87k miles the cylinders were worn by about 0.004" at the top. The decks were not parallel with the crank. Everything else was in good condition.
The engines had poor oiling, with too much delivered to the heads and not enough to the block. Barry Rabotnick "wrote the book" on performance FE engines (look it up), so I took most of his advice on his oiling chapter. After consulting with local builders, I decided on a high pressure oil pump, streamlining the passages, 0.075 restrictors to the heads (0.060 would probably be better), and 6 quarts of 15W-40 in the factory 5 quart pan.
Starting with the cam, I choose a Lunati Voodoo roller lifter type. They have a series from mild to wild and I chose mild. The taller lifters means custom length pushrods and an adjustable rocker set. I chose a PQ set, roller tips. I also have a roller timing set.
The factory pistons only gave about 8:1 compression, not the 10.1:1 as stated in the Shop Manual. Since I kept the factory heads (with new hardened valve seats) we chose new forged pistons to achieve a 9.7:1 ratio. Consider new Edelbrock heads and you'll be able to live with 10.5 or so.
I chose a FAST EFI system with a throttle body. Consider their sequential system instead. The factory dual plane manifold worked terrible with this, so I ended up with an Edelbrock Victor single plane. The FAST sequential setup is based on the Victor.
Sanderson Hot Rod headers. 2.5" dual exhaust with H pipe. 14" Borla mufflers mounted before the rear bend and Hushpower rounds mounted in the stock resonator position.
MSD Ready to Run distributor. I have a 6A ignition box but its not completely necessary. I run 15 degrees initial advance plus 19 degrees vacuum at idle. My centrifugal advance adds in up to 18 and tops out at 18 degrees. Easy starts, no ping or knock. On my last tank of gas I achieved 15.6 mpg. This was a good mix of highway and city driving.
I'm running an electric cooling fan from a Mark 8. Used ones are $100 or less and they move a lot more air than aftermarket fans. It fit almost perfectly on my factory style radiator. A control kit adds in another $150 for a good one. The engine does not overheat, and that used to be a recurring problem before the rebuild.
The factory air cleaner is restrictive, and conflicts with the taller MSD distributor. I have a 14" open type, dropped to clear the hood.
I'm guessing that HP has increased from 300 advertised to about 350. Someday I'll dyno that to confirm, but the car moves quickly off the line and will happily accelerate from the posted 70 mph speed limit to faster than I dare.