By system CD you mean the Operating System? Windows? XP?
Was XP previously installed? If so and you're told that you need the disk then you probably need the disk.
You can load a free Linux system but Windows cost money.
http://www.d-a-l.com/help/linux-help/
If you know the manufacturer of the hard drive download the diagnostic from this list:
http://www.tacktech.com/display.cfm?ttid=287
As you mention the connections: if the motherboard cannot find the hard drive then maybe XP is still working.
The connections are pretty simple. There are two that will take IDE cables the Primary and secondary. But the hard drive on the Primary end and the DVD/CD's on the secondary. Check the jumpers for Master/slave settings.
The floppy is a distinct different slot but should be apparent by looking at the cable for the slot type on the board.
Here is a basic guide with some pics:
http://freepctech.com/pc/001/build_pc_98.shtml