Sounds like either a caliper issue or possibly a handbrake issue. thats exhibiting itself when the brakes heat up. I would tend to err to the latter as it sounds like its effecting both sides equally and you'd be extremely unlucky to get 2 calipers stick at the same time.
Can understand its gonna be a right pain to identify though if it only happens when run for a few miles.
I suppose the only other thing (really remote) it could be is the master cylinder as I beleive they normally apply the back before the front so if the pedal isnt returning fully then it would be the back that has some pressure first.
Understand the feeling of
the brakes at the moment are the one bit my car seems fine on although not driven it yet to see. Getting a mating that I'm happy with between teh column and the steering rack and the sorting the clutch out have been long and still on-going jobs. Have finally resorted to booking it in for a bit of TLC with Talon sportcars to sort those two jobs out so I can move on in the build.