Reply to Random problems after mod

So I just modified my VCI-100 silver edition with the crappy original firmware using the Arcade DIY Mod kit. I didn't upgrade the firmware.

The buttons work great and everything is beautiful. But I have a couple of weird almost mapping issues that I can't make sense of or correct right now.

First, my toggle button for Effect 3 doesn't work. Instead, it activates the monitor cue for deck A. When I tried to go into my midi mapping to fix this, my computer seemed to be registering the monitor cue button and the effect 3 button as the same thing! Its messing up for both FX banks, BUT, it works fine in the loop setting for my D deck loop on button. HELP!

And even more upsetting, my jog wheels will not scratch for decks A & B. When scratch mode is off, they work fine as jog/search controls. And strange but true - scratch works perfectly in the bottom decks (C & D) when toggled on. I can't figure this out in the midi map. What sucks is that I can't use the jog wheel in FX mode now either. Touching it doesn't turn the effect on, though I can use it to change the dry/wet values. it's weird and i don't like it.

Neither of these issues occurred before I made modifications, but these things weren't involved at all in the mod, so I don't know what's up. I'm worried that I totally messed something up and that these are just the first controls to go. plz help me...