Well, lets start with your BIOS (Basic Input/Output System), this would not cause your computer to slow down. The battery for your BIOS only controls mainly the clock time.
Remove the casing, and check the heat-sink below the fan on your CPU. If this is clogged up with dust, performance will be affected in many ways, overheating, intermittent shutdowns, etc.
Ideally, any drive attached to a PC should always have at least 10% of the total available disk space available. Do not confuse this with the hard drives full un-formatted raw size, they differ upon formatting and the filesystem used.
You should first do a Disk Cleanup, and remove any files/programs that are not essential, or you nolonger use. Once this is complete, then run Disk Defragmenter, this should speed up your system to a degree. You also mentioned a slow startup, this can be caused by too many startup programs or services running upon startup. Check your system tray, and remove any unwanted programs by going to the Start button -> Run and type msconfig then select the Startup Tab. Anything you do not want to run at startup, simply untick, then click Apply and OK. You will need to restart in order for the changes to take effect.
Another issue that can cause slow startups is having too many Fonts installed in your system, either remove them or use a Font Manager program.
If you have had viruii or spyware on your system, you will need to remove them, but before you do turn off System Restore or they will come back if at any point you restore your system to one of the dates when your system was infected. I have listed a few free programs below that will help you.
http://www.safer-networking.org/index2.html - Spybot Search & Destroy - for Spyware removal.
http://www.avast.com/eng/download-avast-home.html - Free Antivirus software (Home Use)
Hope this helps you recover your PC to a working state.