There's your problem;
@Nat67 has been in your motor, messing things up, he even left his signature
Only joking. but seriously; my pressure plate had these marks from "new" too.
So what we'really saying is, your & clavigers pressure plate scratches PROBABLY have been there already.
And probably a red herring.
Notice the way the inside of your front cover immediately in front of the clutch pressure plate has no corresponding marks. Mine was the same.
You'd imagine if something was there to get caught on the pressure plate, it'd have to be jammed between it and the front cover to make them scratches... and the front cover would be scratched too
Re the lifter shaft it can be put back as you say following the manual to preload spring etc. It looks ok there
If i was you i'd pop a spark plug out of each cylinder, stick it in N and put a ratchet & socket on that big nut on the end of the crank.
Turn the motor over CLOCKWISE by hand and watch & listen for anything that might be related to the noise you heard on startup before.
You can also get a good eyeball of the timing marks now you've the front cover off.
What's the green stuff in your motor - did you put the coolant in the motor and the oil in the rad?
Just teasing again.