I'm trying to put together an old computer, an so far its gone really well till this one road block. I've used a bootdisk bootwindows 98 in the command prompt and have followed as best I can the directions on using it. At this point my problem seems to be getting the computer to recognize the cd drive as its own master drive, so far all its done is be a slave to the master harddrive on bootup, and from what I read on some instructions I need to copy files for the cd drive to auto run an operating system disk. I'll probably figure it out eventually but help will be greatly appreciated and save me some time

You have the CD and hard drive plugged into the same IDE port. Put them on seperate cables, one on each port.
That said, it doesn't really matter if a drive comes up as slave or master, so I'm not sure what the roadblock is. If you want it to boot off the CD, you change the boot order in setup.

Try one of these bootdisks. They should, allow you to use your CD.

This one, will read your CD.