If you're saying that windows is loading up, and then it stops loading and freezes (as is, it doesn't reboot or anything) then its hard to say. From this limited info, I would say that there's a problem with windows, it doesn't just stop loading for no particular reason, least of all hardware.
If it were hardware related, its probably HDD related, anything else and it wouldn't even start loading.
If it is restarting, not freezing, you might have installed your new cooling system incorrectly, hence it overheats before windows loads, and reboots.
Until you can tell us more about the system, its hard to help.