Fits file re-alignment
I ended up making my own small code that you can find here: 
     https://github.com/crhea93/AstronomyTools/blob/master/Astrometry/Correction.py

Essentially, after inputting at least 3 matching target (found by eye in DS9 for example), the program will calculate the mean offset and apply it to the target image. The output is a new fits file of the target image with the proper correction.