I would also suggest trying other pre-built frames with different geometries. Get your measurements, then see if anyone makes a bike with that geometry. You might not need a custom bike, just one that truly fits YOU!

When you're working with your local LBS, do you get a feeling for what's not working on your current bike? Is it too big, too small, reach too high, too low, seat position okay, etc? You might just need a new bike that's the right size for you.