the problem may in fact be something other than the wheel balance if they did charge you for it (and hopefully actually did it). if you're used to modern bikes, much about the suspension will feel strange to you.. the overall state of suspension can cause strange things to happen... loose steering bearings, loose swingarm bushings, etc. not having followed the whole thread, i'll assume you attended to these areas having done an entire build. do you have a fork brace up front? you'll feel a HUGE difference once you do.. also, i'd have to read back to find the answer to these questions, so excuse me if it's in there somewhere, but do you have stock fork innards? stock springs are usually too soft. preload will help a lot of course, but cartridge emulators really help out a lot as well.
you seem gifted with the fabrication. come by the shop and i'll show you a homemade fork brace that i think works well. you can buy the tarrozzi braces for around $100.