It may make a difference, the card COULD be pulling enough power off that line to starve the HDD of power, so if possible, try connecting to another power supply line (I used to use one for the drives and one for the card when I had an AGP setup).
There is plenty of guides on how to tune a system-try Googling phrases like 'PC tuneup' and 'hard drive maintenance' to start, in the meantime a few tips (you probably already know)
Go through the system and uninstall any legacy software you're not using then manually run through the system and delete any files/folders the uninstall has left behind.
Do the same for documents, backing up to either CD/DVD or a flash drive as required.
If you have any files or folders on the desktop they should be moved into the HDD directories proper, items on the desktop are treated as system files and load along with Windows on startup, worse, Windows scans them constantly to check their integrity-a double performance hit.
Depending on you OS Start>My Computer>Right click on the 'C' drive then click 'properties' then 'general' tabs in the dialogue boxes that appear. Use the disc cleanup option to clean out some of the crud.
Grab a copy of Ccleaner and install it. This is a great little freebie and you should run it regularly to keep the Temp and Cache folders clear of unwanted internet crud-it has other tricks like a Registry cleanup as well as secure deletion options.
If you've done the above the HDD should now be fairly clear of unwanted stuff, so now Start>My Computer>Right click on 'C', then 'Properties' then 'tools' run the tests then the defragmenter. Be advised, it can take hours to defragment a large, old drive!
The final trick is the most obvious: Keep the number of open programs/documents to a minimum, it's less of a problem with these modern HAL 9000s we're using but older systems have more limited resources which need to be used with a little more care.
The alternative is to backup your data to CD/DVD then format the HDD and reinstall everything. It's a draconian option but has the advantage of giving you a clean and totally pristine system.
If you take this option you should place an antivirus program on a bootable disc and disconnect the system from the 'net until you have installed both it and Windows-until Windows finishes updating itself the system will be extremely vulnerable so a little extra protection is a good idea.
Expect a long, long update period, the last time I did this with Win 7 it took 3 days for the updates to stop coming!