Never heard of this MOT rule before
I'm assuming a hand made pipe would fail too then unless the creator stamped some numbers on it?
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I imagine the sound you heard was like the first few seconds of this vid?
In that bike's case it was the bottom end on the way out and there was play in the conrod but obviously shouldn't be the case with your bike.
Could be compression related though I guess.. Did you get your cylinder checked for correct sized piston?
Just to chime something else in, my TDR doesn't really have much past 9-10k either, but it seems to be due to a small hole where my silencer meets the expansion chamber. Whenever I patch it up, I get much more pull up the top of the rev range. Sadly my fixes don't last long