What OS are you running?
In BIOS, can you disable CPU Throttling? Or is that even an option? Also, what is your boot-up sequence? Can you have it skip certain test to allow for a faster boot-up?
Most likely the HDD is running in the slowest/most reliable UDMA settings, upping it to the mobo/HDD highest compatible speed will boost your performance hopefully (use the lower of the 2, not the higher of the 2)
Also, are you hooked up to a network or any kind of LAN? My computer takes FOREVER to login when my network is down...but if it's functional it takes about 3 seconds.
Lastly do you have the latest BIOS installed, latest drivers for your mobo, HDD, all of that. Windows update and look for latest drivers for your hardware. An old driver can cause many problems, and a new one can fix them all