ORIGINAL: jedijody
It would seem your initial, and hurried assessment of the problem was incomplete, thoroughness and patience are virtuous Padawan.
Well it ran great 2 days ago. Only the last flight I noticed the shaft being out of line and now that clicking sound

I did a tedious job putting everything together, cleaning, new header nuts etc. I'll take the prop hub apart and if that doesn't reveal a solution the engine is all yours

You have all the parts within reach...