The only wires you should have had to deal with, would have been the CPU fan connection. Unless you removed the board from the case to install the cooler. Did the cooler come with thermal compound already installed? Or did you install your own?
Hi! Sorry for the late response! But yes I did take the entire mobo out for install. I played with it for awhile for the week after I asked this question and ended up reinstalling windows on a new hard drive and transferring files back to the old hard drive and it fixed the problem. I'm not sure why the system would be so off thrown by a fan change, but nevertheless my problem could be considered fixed.