Japanese Mega Drive Controller Ports Not Working

I originally posted this at reddit but was directed here.

Hello,

I have a japanese mega drive model one that I ordered from ebay. It was modded with s-video, and rca audio and video jacks. It also seems to be region modded. The controller port does not seem to work correctly. A button does not work. B button acts as A button, and C button is start. I took it apart and the modding looks pretty subpar. I checked continuity on the controller port pins to the pins on the motherboard after I reflowed the solder on them and they were all good. I also checked the continuity from the controller port pins on the motherboard to their first traces and they were all good there as well. I am pretty at a loss at this point. I took a lot of pictures of the motherboard and uploaded them. I am not very familiar with what the installed mod is doing. Unfortunately it was quite some time after I ordered this from ebay that I was actually able to test it due to a sudden move.

Motherboard model VA4

Pictures of Motherboard: https://imgur.com/a/87bA09g

I added two photos of the lines that I have traced continuity, the only area where it stops is at that little box marked 331. I was assuming that was a resistor and it should break continuity there but I don't really know what I am doing.

https://i.imgur.com/RXnDLcD.jpg

https://i.imgur.com/cuTlPiZ.jpg

I took apart the hyperkin controller, stuck it into the port, and checked for continuity. Pin 7 on the port is beeping on pin 9 on the controller. It does NOT beep for pin 7 on the controller. Could this be miss labeling on the hyperkin controller or is this the cause of the issue? If this is the issue, how do I fix pin 7 going to pin 9 in the controller? What is odd, is that when I check continuity in the controller port, it appears correct, pin 7 on the board to pin 7 in the socket.

Okay, I took apart an official controller as well and it gets continunity from 7 to 7 just fine, so I thought, maybe I just never actually checked on an official sega controller somehow and am misremembering, so I put it back together and plugged it in and tested both controllers and still the same issue, while it was running I checked continuity all the way to ic5 and it seemed good. I am not sure what else to look for.

Also, it happens in both player 1 slot and player 2 slot.

I have tested with an original sega controller. I have been testing with my mega ever drive x7 and also an original sonic 2 cartridge. I was just now measuring voltage while it was running on the official sega 3 button controller plugged in and opened. I get -4.92v between pin 1 and 8 and nothing anywhere else to pin 8.

Something else I just realized is that actually it seems to be outputting both select pin values when you hit those buttons. In Sonic 2, hitting C causes a jump and then pauses the game right afterward.

Unfortunately I don't much know what I am doing with a scope yet. Here is what I got from pin 57.

https://imgur.com/kTFNeq7

Well, looking at this more closely, it looks like that is set to 100mv and nanoseconds scale, so probably useless. I would imagine it should be jumping 5v or so, not 100mv right?

Looking at the scope it seems to just stay at -5v or so all the time with just little fluctuation.

I took apart my working model 1 usa VA3 board and measured the same point 57 with the scope, it looks like it has regular dips that just don't happen on the japanese model: https://i.imgur.com/xM7gvOZ.png

Could this be a short somewhere or is this ic just trashed?

Edit1:
So from info online, I have found that the TH signal, (select/mux) comes from pin 63 on the 68000 and runs into pin 71 on the 315-5309 ic5. I checked and I do have continuity there. Is there any other place where TH is generated that I could check?