Re: master cylinder problems.
On some master cylinders you can adjust the reach to the lever with an adjuster that alters the length of the piston actuating rod. People who like a long reach have been known to adjust this to the fully "out" position at which point the lever reaches it's stop (especially possible with an aftermarket lever) and if you turn it any further you are actually pushing the piston in....and it can no longer return properly.
Becomes a problem when the brakes get hot, the fluid expands a bit and the brakes can't release.
I know this from experience. Being stuck in the middle of the Cadwell Park straight on the 3rd lap with a front brake jammed on so you can't even get off the track is not something you easily forget...!
To answer your question the master cylinder not being standard won't be your problem. You either have binding brake callipers (you say you're checked that) or the master cylinder isn't releasing properly. Take the lever off and check the piston is coming fully back (you may need to remove the outer rubber cover). You will see if it isn't because there will be a witness mark on the cylinder. If in doubt rebuild it. Personally I wouldn't have used second hand brake parts without servicing them anyhow.
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