Good it's running better now. It needed the exhaust on and the TPS set / ISCV reset to get here.
Secondary TPS also checked for correct setting? Throttles balanced?
I would also be concerned re the PC3 relevance and the maps suitability.
It sounds a bit weak although running ok.
Why is it 0.601V in the 2nd screenshot, even though the target is 0.72V? Or is that just screenshot taken wrong time.
Anyway re the clutch I would strongly suspect the lifter arm and lifter shaft positions are not right. There is a spring on the lifter shaft and when you disconnect the clutch cable (e.g. when you are selling the engine to someone) it will spin the lifter shaft out of printed position and leave the whole lever feeling impotent.
The noise if makes when put into gear, might be just dogs hopping off the gear as it hasn't engaged fully.. there should be a firm clunky as it goes fully into 1st.
Also even if it is in 1st fully, the rear wheel has freedom to play about on the slack in the drivetrain and the noise could also be the dogs hopping off both sides of the windows as the engine turns the trans and the rear wheel has no resistance to hold it against the driving face of a gear window.
You took off the front cover and all was ok with the lifter shaft and lifter piece?
Correct reassembly of these and your clutch lever etc should work right