No smoking gun there....
Why do you need a clutch basket tool? You don't to pull the steel and friction discs. Just the bolts on the end.
As for metal flecks, you may have made those simply by removing the bolts. And if the caps are not loosened in multiple steps the cam could easily knock a chunk off a cap.
If you can get the chain out, you can spin it by starter and maybe listen for noise? As in no valves in motion.
I loosened and re-tightened the bolts in 1/4 to 1/2 turns, going left-right-left-right.
The clutch tool would be needed for clutch removal. Why would I remove the clutch? Because I've just reached my wits end with this issue, and the only solution I see is to remove all the parts until I find "it".
I do appreciate a lot all the replies I've gotten for this, but today it's over 1 month since I towed the bike home and pretty much all I found broken is one half-worn cam chain. Overall I must have over 60 hours put in this (including all the online research I did, and yeah weekends were fun, just ask my GF), still counting, and still with no clear diagnostics. Had I just taken out the engine, and fully torn it apart, along side with all auxiliary parts, in 20 hours maximum I would have exhausted all possibilities, and also fully overhauled the engine.
As for running it by the starter, I did think about it but not sure it'll reproduce the noise, plus there is the risk of burning it after keeping it on for minutes.
Sorry for the rant but I'm just frustrated with myself, firstly for being too cheap and not buying something with a higher chance of very good operation (as in newer, from the original owner and lower mileage), and secondly for wasting so much time in a futile effort to save time.
The oil has almost fully flowed through the paper filter, still having about 50ml left, which should be drained by tomorrow. From what can be told by tilting the mixture a bit, there are a few silver, gold and black (plastic) tiny particles. I'll also cut open the oil filter tomorrow.
Next things to come off are the oil pan, and the engine head (yeah, I'll buy a new head gasket as well

). Then it's the crank case and transmission.
Getting close now - that metal may be the cause of the stretched timing chain too.
Need to find more of it and where it came from.
Apart from running out of parts to check I'm not really closing on anything with this.
The most likely cause for the chain stretch is the tensioner, which by the marking on it's shaft I could tell that at certain points it got stuck (gliding in steps rather than linear), allowing for a tiny bit too much slack, which in time had a cumulative effect.
What is that last picture of?
And that rear cam chain guide has got some serious wear where the chain rides.
You can see the wear (from the chain) and then the lip, (when it was new), besides cracking.
Ok, I'll buy a new guide as well...
The last pic is a side view of the part of the chain guide which gets pushed by the tensioner.