Not enough details here.
So your original config was motherboard (44pin) - 8.5 GB 2.5" HDD (44pin, master) - CD-ROM drive (40 pin, slave).
Then you disconnected the CD drive and added another HDD. How big is the new HDD ? What kind of HDD is it ? 3.5" 40 pin or 2.5" 44pin ? If 44 pin, how did you connect it to the 40 pin connector ? How do you supply it with power ?
Finally you disconnected everything and reconnected it like this:
Motherboard (44pin) - new hdd (master) - CD drive (slave, 40pin).
How is the new hdd which was previously connected to the 40 pin connector now connected to the 44 pin connetor ? How do you supply it with power ?
Does the original config still work ? Is the old HDD still recognised ? Is the CD drive recognised when the old HDD is connected ?
Is the new HDD recognised when connected as slave toghether with the old master HDD ?
Does the new HDD spin up when connected to the IDE cable ?
Does the CD drive open its tray when connected to the IDE cable ? Does the CD drive react on Ctrl-A-A ?
Does the new HDD react on Ctrl-A-A (does the spinning noise change) ?
Well, a vague conclusion:
If the old config does still works, then there is an issue with the new HDD. If the new HDD is recognised when connected together with the old HDD, then nothing is lost.
Mayby it simply is the well-known slow-spin-up-and-spin-down-during-reset problem. So if you hear a difference after Ctrl-A-A, you might want to try to cut the reset line of the IDE cable. (Get a spare cable first for the case you cut too deep.) Then the HDD should be recognised after a reset. And the slave CD drive will probably be recognised, too, once the master works.
Bye,
Thomas