The third gear issue is a common problem but usually linked to 2009 bikes and between a particular set of engine numbers, from memory, roughly 6200 to 9200. Sad to hear that gearbox issue can still be playing Russian roulette with newer bikes.

I read you changed the fuel pump.....I / we would like to know why that was done and was the replacement a genuine Yamaha part or a specifically recognised part?

It's great to hear that a bike has been 'used' and has done some battle mileage.

As for the valves, where they set on a cold engine and did you do them or where they done by someone else who said "they were done"?

Also the TPS, what angle did you set that to?

Your list of work done ....to me....sounds like the exact same list of, individual, possible causes that would bog an engine down at high revs, especially poor valve (may be too tight) gaps or a Chinese fuel pump not delivering or a TPS set incorrectly.

__________________
I have a lot of growing up to do. I realized that the other day inside my fort.