Bones, at least you're doing your converting in the "right" direction (flint to percussion), in my experience anyway, and for what that's worth.
I got my first ML rifle as a trade at a pawnshop, and thought I'd made a heckuva find: a Lyman GPR .50, with both flint and percussion locks, drum, and all to "fit" to the flint breechplug.
Well, apparently, the original owner attempted to do his own converting, and it didn't work out so purty good.
By the time he got done, he had the touch hole wallered out so bad after drilling out from the stock Lyman 6mm to 1/4-28, the shoulderless touch hole liners that came in the trade would wiggle their own way right into the chamber if not watched closely, and the percussion drum never would tighten down and stay put under recoil.
He also had "fit" the stock Lyman percussion lockplate to the position of the drum inserted into the flint touch hole... and NOTHIN' fit right (the Lyman plate is pre-inlet for their percussion breech/bolster, and the flint breech/touch hole is quite a ways forward of where that lockplate inlet lines up). The drum inlet he'd filed into the lockplate looks like he'd done the job with a chainsaw, and did nothing whatsoever to support a drum.
And, to top it off, with the flint breech touch hole being so far forward of the percussion breech touch hole, hammer-to-nipple geometry never would line up, even with heating and bending the stock hammer.
With a lot of reading here on the forums, a lot of time spent simply allowing ideas to gel into plans, and an awful lot of trading out parts, I've finally got a flint GPR that shoots consistently, and am most of the way toward "fixing" the percussion system (not a big deal: fit a 9/16" diameter Leman drum; drill/tap for the nipple; bend the hammer just a tad, to fit the new drum & nipple angle).
Eventually, I'll simply buy a stock .54 GPR percussion barrel, and leave the flint-breeched .50 I've got for flint only.
As to my earlier comment about converting in the "right" direction: from what I'm told, converting from percussion to flint is often much simpler than the oppostite; if a guy builds a rifle from ground up for a percussion system, then converts to flint, although the lock conversion can be time consuming and labor intensive, at least the touch hole position remains the same (unless, of course, you have a bolster blocking your view... ).