Sweet so all problems resolved.

Checked the manual and the proper re-sync process is:
1) Press 'unlock' on remote.
2) Insert key and turn 1 notch.
3) Turn key back to off and remove.
4) Press either 'lock' or 'unlock' to complete the process.
5) Get back on with your life.

Window auto up/down restore process:
1) Close affected window all the way.
2) Pres 'Up' for 1 more second.
3) Test auto up down feature (will be restored).
4) Repeat for all remaining affected windows.
5) Rejoice.

I was just a little surprised because I unplugged the battery when I installed the boost gauge and did not run into these issues.

If anyone knows of any other known issues after disconnecting the battery, which I may not have encountered/realized yet, please let me know.