I'm making some progress.
I booted into Safe Mode and followed this guide
to disable all my start up services but windows ones.
I can now boot into windows normally, which makes me think that maybe this isn't my HDD and it has to do with some software I have installed. I am currently using WD Lifeguard to fully scan my HDD for errors (to see if it was just bad sectors that my SSD inherited) and if nothing comes up I'll have to guess and check which program is interfering I guess.
The strange thing is that I already clean installed windows about two weeks ago because of this same problem and now it is back again. That makes me think either my HDD is going bad (Which is why I thought to buy this SSD) or some software I installed recently (Pro Tools 8) might be interfering.
Thanks for all the help, you rock!
Edit: Does Repair installing from Windows completely delete all my system files? Meaning that if I have software with settings and Licenses (or whatever they put in there) saved in the registry that I will have to reinstall all those applications?
Double Edit: I just finished the Extended Drive Check with WD Lifeguard that said it "Passed," (pretty vague) but I guess that means it isn't an issue with my HDD.