I found the tensioner update supplement over on Honda Twins. I must have never seated the tensioner slipper properly, because it was definitely too high and was likely caught behind the lower damper.When you noticed the tensioner loose, did you check to make sure it was set to be tensioned? Did you notice if the bottom of the tensioner is seated? Check the piston skirts too. See if they have any marks.
I haven't read through the thread so discount this if irrelevant, but that noise sounds very similar to the noise I heard in my engine after an overbore and rebuild. Turns out I'd installed the wrong head gasket - I installed the OEM diameter gasket rather than the overbore-specific gasket. The noise was the pistons coming into contact with the inner metal rings of the too-small gasket.
The tensioner retainer on my bike looks like the first (top) one in your photo. It has a thin side and a thick side - I installed with the thin side towards the center of the engine. Is that the updated version?
Head gasket is new: 69mm x 0.042'
For what it's worth; when @Hurco550 and I installed the pistons and bored cylinders on my engine we were about to button it up and discovered that my copper gasket needed just a bit of "adjustment." Things looked pretty good and lined up, but the bore cutouts were a tad small. Levi cleared things up w/ a Dremel. You've had yours apart and now back together so I think you'd notice a bit of "mangled" gasket, but I thought I'd mention it anyway.
If you have the 'straight' top holder it's the early style and should be changed. The 'cup' part will have the 'thin' side towards centre of engineI am open to all suggestions. I didn't notice anything with the head gasket when I was reassembling. But it is worth taking another look at it.