I had a stock, and I believe original, exhaust. I bought a complete NOS fording kit still in the box with the template. Mine was short about 1". So I moved the fording pipe to fix it.
Probably a stack up of tolerances. I suspect the original pipes were not cut to high accuracy and bent on a CNC bender. Same goes for location of pipe hangers, etc. These were probably tacked into place with a 1/4" tolerance. Even how far the pipe engages into the muffler can throw you off a bit.
Scott - East Coast Kaiser