Just got a call from the dealer and they said that they spoke to the paint dealer for the MOCO some Thomahawk, and that there is too much clear coat on the bike. They want me to get a estimate to get that buffed out. They said that will do it, and they will pay for it. I am not a body nor a paint man, if there is one out there does this sound like it could be the issue or not and is this the fix.
No way. Absolutely positively no way. You can not be asked to take on, nor should you accept, the responsibility for the work. Granted, within some latitude the manufacturer is allowed to mandate what warranty handling procedures will be. That doesn't include, however, telling you go somewhere else and then be repaid for it.
First off I've never heard a major manufacturer suggest such a thing for issues they could in some way handle themselves. That being so I would be terribly suspicious that this is actually coming from the dealer rather than the manufacturer. He either didn't like, couldn't work with, or was afraid to pass on what the MoCo told him; or he never made the effort and is looking and hoping for an easy solution. In any case it sounds like a pacification response to occupy time that might (he hopes) accomplish something in the process.
If you're even considering this then get the instruction from the dealer in writing. That way when or if it still looks crappy (after what will have to be a heavy buffing) neither the dealer nor the manufacturer can try to abey the claim because you or your guy have damaged the paint. That is the biggest fear in this scenario. Product responsibility is being shifted to you.
They're asking you to work on paint that is their responsibility, with your choice of talent; thereby accepting all that responsibility. For accepting all that responsibility your only remuneration is repayment out of the dealer's pocket for a buff job. Get it in writing stipulating that the work itself is approved and on their instruction, that the shop acceptable to them, that if this does not solve the problem they agree to replacement parts and that a definition of an unnacceptable result includes so much buffing that the clear is too thin or gone. Without that last part you've given away years of longevity in the painted finish of your new bike.
If they're serious about asking you to do this then none of those provisions would bother them. They'd all be part of a logical and acceptable process. If the dealer won't write that letter, however, then RUN AWAY.