Okay, figured it out. It
was cam chain slap. To begin with when I pulled the rocker cover I thought it was the rocker arm shaft because I found this mark on the inside of the rocker cover:
Where I had welded the bearing in looked like it was rubbing slightly so I filed it down. At that point I thought my work was done.
But when I peered down the cam chain tunnel I say that the tensioner plunger was no where near the tensioner blade:
I was wary of over tensioning the cam chain because on a certain stroke the cam chain seems to push against the tensioner and get taught.
After a quick Google I found that you should set the engine to top dead centre to tension the cam chain.
I was doing it on the other stroke where the chain was at it's tightest. I didn't want to ruin a new cam chain by over tensioning it.
As it rests the plunger is just up against the blade:
The noise was the cam chain slapping against the tensioning blade at low revs, like when the engine is cold.
The cam chain still feels loose, it feels like I can almost lift it off the sprocket with my fingers but not quite.
I might tension it some more but I don't want to over tension it. Strangely the whole time it was loose I didn't get the valve lash sound that I got last time.
Maybe that sound was just the auto tensioner assembly rattling around rather than the cam chain itself.
And as for the exhaust side rocker arm even after sanding the weld spots down there still feels like there is a vibration going through it compared to the complete smoothness of the intake side.
Maybe it is due to the decompression mechanism like on the KTM 690s.
Anyway it's nice to have a normal sounding motor at start up now.