I gotta think all of us go through this exact dilemma. I have a numbers matching 4 speed '65 with about 96k on it (changes as I drive it). It runs pretty good, I don't drive it very hard, but I will rebuild it,if it ever comes out. Just when, is the question. My thought is to pull it & the T10, spray it with a preservative, bag it, and store it in a corner of the garage until I can rebuild it the way I want, about a $7-9K project, with me doing all work except machine shop procedures.
In the mean time, a crate engine or build up of a Big Block Chevy will be installed with 6 speed or 5 speed tranny behind it(yes, I know, that's a $15k project on its own). I like the idea of being able to beat the Chevy engine like a rented mule, and not hurting the value should I lunch it. I'll keep the 401 preserved and safe for the next owner/cork sniffer. When the time comes, swap the Buford back in, drive it nicely, and save the Big Block Chevy setup for another car. At that point it'll probably get sold as a well restored '65 GS. I have tubular control arms front and rear and upgraded suspension, but have all the original crap. Paint will be the stock color, interior will be original, etc.
If you pull an engine, you need to at least change the timing set, check the cam, check the heads/valves, check the lower end rod & main bearings, check the distributor, replace the water pump, oil pump, and all gaskets. Radiator needs to be checked out, all hoses, belts etc. replaced. It's usually a small thing that begins the cascade of a catastrophic failure. I say all this because my biggest fear is lunching an original block, and ruining the car's value with it(hence, the BBC plan).
Good luck with your project...