Yes, it could be bad flow on the CPU or graphics etc, often this can happen with extreme heat/cool cycles, usually more with graphics cards (the one not part of the CPU)
Did you test the BIOS I sent you again first, with all the external display ports? May be best to leave that red chip alone then, hopefully it's "Current" contents are OK
Some chips it's just near impossible to read or write too while connected, this can be common sometimes, so this must be one of those situations for that chip.

SuperIO probably does not need reflashed, that would be rare, but yes, of course, sometimes this can fix things too but it's tough to do.
You can use your programmer, you just need to make your own cables and connect to the KB ribbon cable in proper manner.
Of course, you need to find specific info for this model for that purpose, at least they posted the schematic there
Ohh, I see they did not, here you go, at vinafix, EC FW there too if you still have time left, if not here in post #18 you can get the PDF after joining, if you need me to grab for you let me know)
I would join that forum you linked and ask that user directly for more info, especially since those are all posts from this year.
I tried to look around for guide/method/info on this for you in regards to this model, but no luck, so asking that user directly is your best bet

* Edit -Leave the red chip alone, and hope it's got valid info in it now, I think it did originally anyway. If anything, try to put back to original and leave.
What you mention about the LEDs can be sign of a short, or incorrect connection, so be careful.
Yes, if you know how to solder well, you can desolder and program the chip, but it's in a tight spot and put on with Lead Free solder, so if you are not good at soldering and desoldering I would leave it alone
This is not part of the problem anyway, at least was not, but now could be blank or partially written