it would appear that you've managed to catch your self between the proverbial rock and the four letter hard place. i make several assumptions:
1) that you have already inlet the lock into the stock, so you're stuck with the location of the lock as it relates to the barrel.
2) that you've already inletted the breechplug tang into the stock, so you're pretty much stuck with the location of the barrel as it relates to the stock.
if either (or both) of these assumptions are not true, then you have no problem: simply move the lock foreward or the barrel back, so that the center of the pan is about 1/8 inch in front of the front face of the breechplug. get a good touch hole liner (i like white lightnin') and install it so that the touch hole is centered on the pan and slightly above the level of the pan. this is the much touted 'sunset position:' the bottom of hole wants to look like the sun touching the horizon at sunset.
if, however, you're stuck with geometry that doesn't support this, do not dispair. at least one other guy (that would be me) has made the same mistake. what you should do is (with barrel and lock in the stock) mark where the touch hole should go on the barrel. figure out how much of the breech plug occludes the touch hole. in my case it was only about 1/8 to 3/16 of an inch.
if you're way back into the threads of the breechplug, you're in big trouble (more on this later)
if, however, you have at least 1/2 inch of threads which engage the barrel, you're probably safe (disclaimer time- if you blow yourself to bits, i don't know a thing about it.) so, assuming that you have enough threads to work with, go ahead and drill the clearance hole for the liner with the breech plug removed. put the plug back in and mark the threads you'll need to file away. i tried to make mine as smooth as possible without removing too much material- this will minimize the possibility of a live ember getting caught up in the rough bit between the touch hole and the barrel. once you have filed the groove, put the breech plug back in the barrel and visually inspect that there is a smooth channel or groove for the powder to make good contact with the touch hole. if you're happy with it, go ahead and tap the threads to the liner and put it in. use anti- sieze goop. you should be OK.
as regards the foulding issue, yes, you will have a bit more trouble getting it super clean, but (always a "but") you should get or you should already have one of the clever little clamp- on cleaning attachments (Track of the Wolf has the best one i've seen- it's called a flush-flint, and it's on page 401 of their cataloge #16- costs about 16 dollars and is well worth it) the use of the flusher and warm water should make things go well.
Now the bad news: if you're too far back on the threads of the breechplug (i.e. you don't have at least 1/2 inch) you should give serious consideration to moving the barrel back. Much easier if you have a paralell sided barrel- if you're using a swamped barrel, you're in very even bigger big trouble. i have heard of builders using brass inserts between the breechplug and the barrel, but it's not a trick i would try.
i hope this clears thing up a bit. the two things to remember is the half inch deal, and make the groove (if you do have to cut one) as smooth as possible.
good luck
MSW
FOR SALE Lyman Great Plains Rifle. 50 Caliber. 1985 Build Date