This really sounds like there are some small differences in the thickness of the new clutch disk or in the geometry of the new pressure plate. Also, did you mention that the flywheel was newly-machined? Any idea how much they took off? The pressure plate multiplies any thickness differences.
Not to ruin your day, but there is another long-shot possibility here. One of the engine's main bearing shells has thrust flanges on it to keep the crank in position axially. The flanges can wear out - allowing the crank to gradually move forward, away from the release bearing. On some engines, the pistons and wrist pins can tolerate this for a while without symptoms (except clutch adjustment). It's not a good way to run because crank thrust bears directly against the iron web. Tractors with separate lever-operated pto clutches often came with a warning not to constantly run with the pto disengaged - because the clutch spring force was always pushing the crank against the thrust bearing.
As always, prompt cheerful refund if theory is bogus. Dick B