It sounds like you might have two different alignment issues.

The first is your string test one. That the two drop outs are not on center WRT the main triangle is the easier one to correct. Although i am confused a bit if this is actually what's going on. You posts have been conflicting, #7 says that you did align the drops' center WRT the main frame "aligned dropouts relative to frame's center using correct tool (shop quality not DIY)". Yet #9 says the rear end is still off "left side: 3.4cm -ish right side: 3.9cm -ish".

The second missalignment sems to be that one drop out is below the other, think of it as one seat stay is longer then the other. This is the more challenging one to correct.

But again given your discriptions and conflicting statements anything is possible. What is not at issue is that your using tires and fenders that really weren't taken into account when the frame was made. The PX-10 is a racing bike and has reduced clearances by purpose. This bike likely came with 25 wide tires, at most, and fenders were an afterthought given the bike's intention. Not saying that your combo of parts won't or shouldn't work but that you've used up all the fudge factors and hearing that you've got fender rub is not surprising.

Again I'll say that if you want a real and full understanding you need to get the bike to some one who has done this stuff a bunch and can seperate the various factors. then they can give you the corrective options, some might be simple cold setting, others might be more involved and invasive. There's no magic about this, just carefull investigation and skilled efforts. Andy.