To be blunt it's a hot mess, sorry. Wires are too thick and disorganized, everything is covered with (burned) soldering gunk and you can't really see what's what.
You just have to check continuity again to see what you have missed. Won't be easy. Use the photos you made before you started the repair.

I checked continuity between all points and all check fine. The burned stuff is flux, but I'll do try and clean, if that could be the main issue that's causing this.

As for wires, I used mostly laptop speaker wires, as this is all I had on hand. I think I do have some ASUS IDE cable I cut up eons ago, but those usually have wires so crappy that they don't even stick solder.

Agree with Miphee that the patch work is quite messy. If you could find wire wrap wires, it would be much neater as they are quite thin. Keep the wire length as short as you could, and clean up the flux with alcohol and it would be better. I saw corrosion at the top side of the board near the battery too. I would clean those up and check the connectivity of these traces. Back to your keyboard issue, take some time to trace the clock and data lines starting from the keyboard connector and check their connectivity along the way.

Check continuity between the 5 keyboard pins and the KB controller.
Here is one of mine as example:

1. - (seemingly NC)
2. pin 5
3. pin 39
4. pin 20
5. pin 1