I don't have a wealth of experience building from kits, but I have built a few from Tennessee Valley Muzzleloading, two from Track of the Wolf, and a fowler kit from Brad Emig at Cabin Creek. Being a lefty, these kits have needed the lock, side plate, trigger, trigger guard, butt plate, and ramrod pipes inletted. It seems to me from my limited experience that the lock and its pan determine the placement of the touch hole, but I suppose it could be done the other way around by having the lock inletted and touch hole drilled by the kit supplier. The proper alignment of breech plug face, touch hole, and pan must be as precise as possible for the rifle to fire effectively without hesitation.
I've not been disappointed when dealing with the folks at TVM, and I would suggest calling them with your concerns. The "kits" from Track of the Wolf have been complete, but are simply a collection of parts. Brad Emig is a fine gun builder, and always willing to offer help. I did have some issues with the inletting of the butt plate and trigger guard of my fowler kit.
The main issue with building a flintlock is never, never rush any step in the building process. You must take your time, and think your way through each stage of the task. I highly recommend Chuck Dixon's book on building a Pennsylvania longrifle, and a visit to Dixon's Muzzleloader Shop would provide an opportunity to look over an extensive collection of custom built rifles. And, a July visit to the Gunmakers Fair at Dixons will provide a special opportunity to see, first hand, the work of many of the country's finest gunmakers.
Enjoy the gun-making journey! It is a tedious, time-consuming, but thrilling process to experience the collection of parts becoming a completed long gun. Good luck with your build.