One more thing- I did some research and it seems that the piston rod bolts are the elongating type, therefore really non reusable.
This sucks so much, if I order new bolts it will take another month or so to get them

((
The options are:
1- reuse them and risk them breaking and terminating the engine- this seems the riskiest option
2- remove the cylinders with the pistons still fixed to the crankshaft, I've seen this done before but it has quite a risk of bending the rings when reattaching. This would allow full cylinder inspection, but no rod bearings access
3- leave the pistons and cylinders alone, only removing the crankcase and checking what else is left, mainly just for play as the crankshaft won't be able to be removed
4- leave the whole ****ing thing as is, refit everything as soon as the new parts arrive (cam chain, guide, etc) and pray that the engine won't make that noise, and if it does, restart all the tearing down, as there is no way I'm risking riding with an engine that has a high chance of failure/seizure. It will cost me a new head gasket and am additonal number of hours of my time
5- order and wait one more month for the new screws to arrive, saying goodby to any riding for this season
Got over 120 hours in this, at the current moment, and still don't have all the tools, still don't have all the parts.... I do enjoy projects and wrenching quite a bit, but in all honesty, this has gotten past "fun". If I were more rational, I'd just do some damage control and either swap a full engine from a low mileage bike, or just part the bike entirely. However I am not that rational, and after going this far, I'm 100% determined to get this bike fully functional, even if it costs me 10000€ more and 500h more of my time, and taking 5 more years.
My GF told me "congrats on your bike for life!". I asked her "what?" "...well. after all the time and money you've spent on this bike, there's absolutely no way you'd be able to get it back, if you decided to sell it. So only thing left is to keep it for life". And though she's not up to date with all the money and time spent into this, the affirmation is correct. Factoring everything, it has gotten past it's original list price...