Ah the forever unanswerable existential classic and vintage question. Some bikes are worth more as a whole, but rarely.

Part it out, make some money and build it with the components you like to use and enjoy it. If you are they type that will feel guilty every time you ride it then sell it.

Your answer will change as time goes by. One day you may wish you had the bike all original, but you don't need to save all the parts for that rainy day if the money will allow you to make the bike the way you want to enjoy it now. Now is what is more important.

BTW, the vintage road market is not inflated atm if you ask me. It corrected around the same time the recession hit. In the years leading up to the recession prices on many things were often double, but the supply was more limited. Now the bandwagon is full and the supply is good. The demand does not seem to be growing anymore and the fixed gear craze has equilibrated. This is neither a good nor a bad time to sell in my opinion. You could wait as I am sure there will be a slow steady climb over the next 10 years.

It sounds like your bike would be better parted out. Based on your description of less than desirable paint my choice would be to part it out and build with components that would make me enjoy riding it. Unless it is a 60-63 cm frame then you should sell it to me, expecially if it has fender eyelets.