Keyboard not working after USB port repair. But sort of?

Purchased a Lenovo X1 off eBay (good deal needing minor repair), everything was working fine except for the 2 USB-A ports ( they where in USB mouse receiver surface mount mode a.k.a. ) they got squished in. Tested everything and it was working fine so I configured it for what I'm going to use it for and everything's been working for the past 3 weeks except for the previously mentioned USB ports. just got the connectors in and did a hot air rework, a bit challenging. Now the USB ports work but… The keyboard doesn't!? I have reseated the Zif connector, still nothing. But if I do a hard reboot it works caps light comes on I can enter the bios but after that any reboot or shut down no caps light no keyboard. USB keyboard works on the ports that I just replaced. And the touchscreen works however the touchscreen keyboard (windows 11) makes clicky sounds like it's trying to type but nothing comes out into the password prompt almost like there's a key getting held down but no characters are typed. There is a keyboard test in the BIOS (COOL!) which works fine and all keys are readable no stuck keys from what I can tell. Hypothesis It's almost like it loads up in one mode say PS2 and then the BIOS tests the keyboard and loads another driver up the chain into another protocol which can't communicate.

Edit: Oh yes forgot to mention tested in Linux does not work. On screen keyboard works most of the time and some of the time not but USB keyboard is consistent, not sure if that's a Windows 11 I'm not ready yet glitch.

Oh hey just realized the track point works you know the mouse thing in the middle of the keyboard. I am an IBM / Lenovo convert, but still haven't figured out the track point logistically.

Help?