sudomod

So I had a problem with the software where the pi would boot up and freeze, then I couldn't turn it off. I re downloaded the software, and it fixed it, but now the A and X buttons don't work. I checked continuity on the test pads with the pi, and even the pi and front PCB pads, and they are fine. Any ideas on whats wrong?

Check them to GND, here is a question for you and I think the answer is yes but did you use Flux to assemble the Pi and controller PCB?

Yes I used flux

What do you mean check it to the Ground

The crappy flux you use and seems everyone who has the same issue uses is a type that needs cleaning afterwards. If you see that oily or wet looking residue that is a big giveaway you have flux that is in between the boards and likely shorting the buttons. You need to clean the hell out of that stuff with Isopropyl Alcohol aka IPA then let it try and see if that solved your issue.

What I meant check to GND is use your multimeter to see if the A button GPIO has continuity to any GND GPIO or pad, if it does you could have a short and there is a GND near the A GPIO. Your flux could also be causing a short between those 2 points which is why it's very important to clean it off and not even use it in the future.