If your motherboard is capable with UDMA, the motherboard setup disk should include a PCI IDE CONTROLLER driver for Windows 98. Use auto in your bios setting for IDE0, IDE1, IDE2, IDE3 should be fine.
40 wire cable is good for 16MB/s and 33MB/s (all three connectors are black)
80 wire cable is good for 16MB/s , 33MB/s, 66MB/s, 100MB/s (The connectors are black, gray and blue)
As long as you didn't connect a harddisk to a 40 pin cable that is fine. Don't worry.