So I took the y-axis motor out and took the pulley off of it multiple times - it didn't look bad but I found an aluminum GT2 20Teeth pulley that I replaced it with and it fixed the odd jitters. After looking much closer at the removed pulley it looks like there is a TINY fracture in it that changes the size of one of the valleys and it was just enough to cause issues. This was annoying.

Thank you all for your help.