Youre right.
Thought id give the easy things a go first.

When i say serious wiring issues i'm talking about wires soldered directly to pins and boards, so i cant exactly swap boards over without doing the repinning.

I guess it was worth a shot trying these small fixes, its highlighted the issue is probably with the boards.

You need to get back to basics.
Sort all the wiring issues out first before trying to sort out fine tuning type issues.
The temptation is always there to get things roughly going quickly but sometimes it can bite you hard and stuff something up.