Replaced charging port - Apps & launcher missing, rom & settings present.

A

AC Question

Hi,
First post on android central, even though I've been using this forum for a long time.
So heres my problem.
Basically my charging port was kinda bent, stopped working for a few days last month, til' I stuck a toothpick inside for a few hours to give it some opposing force. so.... I decided to order a new one on eBay (US seller and all).

Some details before I start the core story:
SGS2 I9100 (I9100-T variant), Rooted, CM11 Nightly (20150302), Android 4.4.4


Went on to install it today, noticed the board rev number is different but all in all the same. Installed perfectly, booted up the phone and all my apps are missing.
Only ones seem to be some sort of "minimum" version of gapps. GO launcher is missing, play store is missing etc. Settings, home-screen background, lock-screen, alarm clocks, sms, contacts etc ALL present.
now is the funny part: in settings-superuser list i can see all the apps that have the permissions i gave. app list is essentially blank, except for those few minimal system apps i see in the app drawer, no downloaded apps. I cant install play store from apk (wanted to check if i can re-download my app).

Tried returning back to my original charging port, Still the same issue.
Tried checking if I accidentally popped some flex cable relating to USB/memory. found nothing.
Searched for similar issues, nothing that matches my case, unfortunately.

Please help :(