Ok so I "fixed" that.
Had to reinstall POL viewer 6 times, and it finally gave me the SEID option. I have no idea why, I chose to blame Steam.
(although I think its because I didn't delete all the POL files as the Install from SE stayed in steam folder after removing files maybe I dunno).
Now I get a 37K File check again. So hopefully this works...I made it this far last night and when I went to launch game it told me FFXI wasn't installed, then it told me no expansions were installed, and then I started getting my POL issues...so hopefully its not back to square one.
Seriously **** steam.