I think we all may be confused on what has and hasn't been tried so here are the combinations. They should all be done on the PRI_IDE connector on the MOBO....
First, before you try anything else you say the DVD is functional now so leave it as is. Connect the new HD to the EIDE connector (all drives made today are EIDE) using the 80 wire cable you bought with the HD jumper set on Cable Select. Then proceed to the note below...
NOTE: In EVERY case, boot, go into bios and set the Boot HD and boot drive order. Every time you move a drive that will change automatically in bios and may not be correct. I still think this may be what caused the original problem. And by removing and adding the drive things just got confused from there.
If using the EIDE connector doesn't work then....
1) On the 40 wire cable, set the DVD to Slave and place it on the connector farthest away from the MOBO. Set the HD to Master and place it on the connector closest to the MOBO. (see note above)
2) Swap jumpers on the drives, but not positions on the 40 wire cable. (see note above)
3) From the starting point (1) swap positions but not jumpers on the 40 wire cable. (see note above)
One of the above SHOULD work. If not proceed...
4) Use the 80 wire cable and set both drives to cable select. Put the DVD on the connector farthest from the MOBO and the HD on the connector closet to the MOBO. (see note above)
5) Swap positions on the 80 wire cable without changing jumpers. (see note above)
6) This is going out on a limb, but set one drive to Master and one to Slave on the 80 wire cable. (see note above)
8) Swap jumpers on the drives without changing positions on the 80 wire cable. (see note above)
7) Swap drive positions while connected to the 80 wire cable without changing jumpers. (see note above)
Beyond that, I have a sledge hammer if you want to use it.