This is not a "Buell thing" it is a "motorcycle thing". There is nothing special about the Buell brake system they shouldn't know before they committed to working on it. If they didn't know, they should have turned you away at the door. They took your money and need to provide you the result they promised (a working brake system).

To fix the bike, Lunatic has layed out the clear path of the right things to check. You (or they) can use the close up pics in the first post (below) for proper orientation of the hardware and square-ISH rotor spacers.

https://www.buellxb.com/forum/showth...l-instructions

The Nissan radial caliper shouldn't have the typical 'wrong aftermarket levers on a Buell makes the front brakes lock up' BUT make sure the aftermarket levers you have on that master cylinder aren't compressing the piston at rest. Make SURE there is a little clearance between the lever plunger and the master cylinder piston.

To fix the situation:
1) Know what you want. Personally I wouldn't pay a dime, but thats up to you.
2) Take all your paperwork, have your facts straight, especially what you have already done for them and how much it cost you.
3) SET AN APPOINTMENT and go in and speak to the person in charge. Be polite, and be FIRM about what you want.

Know this: If they won't agree to the terms you want, they won't release the bike to you. That's fine, you can't ride it anyway. Set up a small claims dispute if it's worth your time.
Don't think paying them, then disputing the charges is a good idea either. Your payment (and signing the work order) is your agreement to pay them, so don't do that if you don't agree.

IMO, by them saying "its the master cylinder" then oops, "its the caliper" tells me they don't know anything. Whats next? 'its the brake line'? theres nothing else left to swap!