Assuming your HDD wasn't filled to bursting point, if you think your PC is going to boot faster because you've transferred a big chunk of stuff to an external HDD, then I fear you may be disappointed.
As Gertrude as pointed out, malware is a major reason for slow bootup times in Windows. No AV program is going to catch all malware, especially rootkits. Have you run
Hijack This and submitted the results to the free analyser?
There are actually lots of possible reasons for slow starting, ranging from trying to reconnect a non-existent network link to failing hardware. It might be worth your while running MS's Bootvis -
http://www.majorgeeks.com/download.php?det=664 - which times the various bits of the boot sequence and lets you see what is taking so long. It might be as simple as a corrupted driver.
Good luck!
Mac