Would you consider calling Chris (and talking to Chris or asking Tim to have Chris call you back when he's available) and explaining what you need in a bike, and asking if they can help you get a truly CUSTOM Mondonico with the clearance and braze-ons you want?

Tim was probably right, that you can't modify the existing frame for what you need. Mr. DumpsterDiver was probably pulling a fast one telling you he could do it for you.

Now that you are getting free of the "wrong" frame, maybe ask Chris if Mondonico can create a frame, the "right" frame, just for you?

Not modify and paint an existing pre-made frame, but make an entirely new one to meet YOUR measurements and YOUR requirements?

(Chris and Mondonico did it for Trek, I bet they could do it for you)