So I spoke to David, I could actually call him directly! Very nice of him.

So conclusion:
- C3 bearings are fine, aftermarket good quality ones too, he recommends koyo
- The bearing on the crank is actually a floating bearing! When the crank heats up, the bearing can move. Therefore it doesn't really matter where the bearings sits. It's the position the bearing was in the last time the engine cooled down. The position of the timing/chain gear is more important - and this one is fixed. It's important to measure where it sits before replacing the bearing.

- The output transmission bearing on the left side is a special bearing, and might need to be yamaha OEM.

- He recommends 10W50 over 10w40

- The 3aj gearbox gears / design is still crap. He said it's pretty much a waste of money to rebuild the entire engine without replacing the gears/transmission for aftermarket/newer parts, since the pitting (and as a result lose chunks) will wear the engine again anyway.

Anyway there was another thing regarding this engine, and that is the fact that there's 0.9mm sideways clearance on the big-end. (manual says 0.35-0.65mm). Vertical play is 0, so that's good.
Also, the crank width itself it 75.25mm instead of 74.95-75.00.

My idea was to have it re-pressed -0.30mm so both are within clearance again. However I just came back from the shop and it might be 90euros and he won't have time until 2 weeks.
With the above and the gearing thing, I'm now thinking about just leaving everything as it is (I bought this bike non-running) and see what's what. (with thicker 50 oil)
Will save me lots of euros.....
I'm not sure what the end-goal here is that's the problem. If I want to travel long distances on it in the future it might be worth it.