One problem at a time...not familiar with the Fayetteville, but does it have a barrel and nipple arrangement, or a dreaded Hawken style? And how much off is the hammer...and, by the way, fore/aft or sideways misalignment? If you are just talking about a small misalignment, remove the hammer, clamp it in a vise and twist with a cresent wrench...most hammers are flexible enough to correct a 1/16" or so misalignment without heating/annealing. If it's a fore/aft misalignment. sounds like your barrel may have twisted some...hope not, may be a little more than just tightening it, depending on the type.
Other problem....could be a lot of things, again not familiar with the Fayetteville lock, does it have a fly? Ever had it apart? Sure you put the fly back in? Have set triggers? If the fly isn't in, could be the have cock notch is broken...this can rarely happen even with a conventional trigger...anyway, pull the lock and check for a broken notch, also for bits of wood splinters that may have come loose and lodged in there. If it holds at full cock, not likely the sear nose is damaged, but look at it closely anyway.
PS..one more thing, check and make sure the trigger is returning to "battery", I had a sliver of wood jam one of mine once and thought I'd broken the sear or half-cock notch.