I have also been debating this issue. I have a Springy Mil-Spec that I bought soley as a project piece, but have liked it so much stock that now I'm back where I started. I have one of their Loaded models that I really like, but wanted to try putting one together.
Custom pieces become unique pieces. One of a kind. Especially if you are doing some of the work. You know, the old satisfaction feeling and all. But $1000 is still a lot of money for most. If you bought a second pistol with that money, then you'd have two good guns. Or invest it into something custom and have one really outstanding gun. Tough choices. My initial thought for my project was to slowly put together something. I don't have $1000 to spend so a little at a time was/is much easier to digest. However, I think you reach the point of no return where the time, money, energy invested into the piece outweighs the cost of a new gun, especially custom work.
Good luck with your decision. I know it's a tough one.