So, just a few little tidbits of info on the computer first:
Intel Core 2 3.0ghz, 4gb ram, gts 250, 200gb, 500gb, 2x1tb hard drives, and a 550 watt PSU I believe.
The issue at hand seems to be ever changing. To start, if the computer sits for a while without being on it actually "winds up" to get started, as in all the fans take a while to power up (we're talking 10+ second wait time which is extremely unusual), and once they do, it finally beeps and the bios splash screen pops up. Boots and starts heading towards loading windows...Great, except, it goes black screen and nothing loads...If I leave it loading the black screen and reset the computer it'll give me some nice freaky letters that resemble "BixMi Initialize failed 0xc000009a", the 2nd time it just went haywire.
This all happened right after I took out my TBs (the 500GB is my main) to bring to a friend's. After I put it all together again, it just never worked right.
Now this explanation sounds pretty silly, but really, its about the best I can go about it. I've troubleshooted computers for over a decade and this one has me truly stumped.
Take out all of the hard drives except for the main OS one, see if that works. Then reseat the other drives one at a time and see how things go. This may be a PSU issue like pjmelect pointed out, but with you taking the case apart, unhooking/rehooking things, this may be a drive/cable/motherboard issue as well. I'm leaning towards that before the PSU actually.
So after fiddling with this and reading all your replies, its a weird mixed bag for an actual answer.
Yes, it probably was a power supply issue, but after 2 days the computer is running again, back to normal. I tried booting without any hard drives connected at all (just to see if the winding up issue would be resolved) and nothing changed. Into my 2nd day of fiddling, I realized, user error, caused my windows issue...the dual ram was put in the wrong way, somewhere in day 1.
After Windows started loading properly, even with slow wind up, it took a day or two later, and all of a sudden my winding up issues with the fan ceased. I didn't do anything, the hard drives are all connected still, though this brings up a big warning for me: Replace the PSU soon.
Anyway, thought I'd pass this along in case it ever helps.