I guess you need to match them up to any bike, but when you say Ian you took 1/4" off the left one, I take it that is off the length that goes into the cylinder head? Also what muffler have you used on yours and do you recall what diameter it is.
Yes, I took the 1/4" off the end that goes into the head on the left hand branch. It did fit without but was too close to the downtube for my peace of mind.
The pipe end was also very slightly oval but a bit of careful squeezing in the vice had it nicely round again.
I used a Goldie style silencer, again from jrpclassics, which again fitted well and seems reasonable quality. It sounds nice without being too aggressive.
AFAIK the pipe is the same diameter whether siamese or twin but others know far more about this than I do.
Unfortunately I have a problem with my left hand at the moment preventing me riding either of my bikes......