The cost of decent tubing is in the 10 dollars a main tube range, so the price of the main triangle is pretty minimal. It is easier to start with fresh stuff and work on from there. The rear tubes are a similar price, and there are ways to make top notch rides with alternative tubes like 4130 stays, etc... That might save a few more bucks. Since over half the price of a custom can be in the paint, and that is without having to strip it in the first place, I don't really see the savings or the glory in modifying a frame.
I got offered some tubing sets of Columbus forks everything for 60 bucks. Good deal, but I am sure there are deals like this everywhere once a person has been around the block a few times. I would sure prefer an all new columbus frame for 60 bucks plus lugs crown and drops to recycling some stuff.
In the home shop some cool chopping type bikes can be made, people have done things like tandemize a frame, in which case the front triangle might get away as a reasonably clean unit without any unbuilding. Shortening a top tube changes a lot of stuff.