I can't help (sorry), but there's quite a lot of pertinent information in the zip archive...
You mean impertinent...
Too much irrelevant info.
You found faulty components which you removed... and then you started probing with the unit on and can't make sense of what is happening? A pretty logical thing to do would be to test the surrounding circuitry of those shorted parts. Also, you didn't say if you had replaced them either.
If you can't find anything else faulty, replace them, see if they blow, if so start testing again, if not then I downloaded a zip file for no reason.