First, it might help if you post the make/model of the computer. It may not help us with clones ( generic ) computers, but brand name models generally use the same settings which can be looked up easily.
Take her apart one more time. Look closely at the board, and look closely at the Chips. You may very well have a puter that was a SX to begin with, and was upgraded with an overdrive chip to 486DX. Look to see if you have a chip marked sx. Also look to see if there is one with a cooling fan, or heat sink on it. That will be your DX or overdrive chip. Somewhere around them will be a jumper that should be set to DX33/66/etc.
On your hard drive, make sure the jumper on the end between the power plug and the pins is set to MA ( master ) not SA or SL ( slave ). No one uses CS ( cable select ) anymore.
Plug in the ribbon cable with pin 1 towards the power plug, and make sure pin1 is in IDE1 on the board. You can see a tiny number on one corner, or you may see a 40. If all you can find is a 40, pin 1 is on the opposite end. You can tell pin1 on the ribbon cable because it is usually marked with a red or blue stripe.
Do the same for the floppy drive, although you don't have to worry about a jumper setting. Use the end of the ribbon cable that has a twist in it for the floppy end, not the motherboard end.
Make sure your video card and memory is seated. Then, look closely for a jumper that is marked CMOS CLR or something similar. Pull it off, or put it on, as the case may be, and power the system on. Turn it off, and change the jumper back.
If the system has a removeable battery, you can do this also by removing the battery, and let the machine sit for 5-10 minutes.
When you turn the machine on, you should see a message in the upper left hand corner. This will tell you what bios you are using, Award, Phoenix or something similar.