As the MadProffessor said, 1/4x28 thread on the nipples in GM barrels. I'll add that Treso brand nipples are also excellent choices.
GM had a problem a little while ago in which some barrels were delivered which had metric thread nipples installed in the SAE threaded barrels; they also delivered, as I understand it, some barrels with helicoils installed in the nipple holes. These problems are readily apparent to inspection with the naked eye, however.
You extended your question to other barrels as well; since the thread used on other barrels can vary from the GM spec, I presume you were looking for a brand recommendation only for the other barrels. I am partial to Tresos, but have no bad things to say about Hotshots or other brands.
How hard to convert to flintlock? 'How hard' depends greatly on your level of experience with guns, and we have no idea what that is. One of our longtime forum members, roundball, has much experience in this area and can be counted on to provide some good advice; if he doesn't see this thread you might ask him directly via a private topic posting.