Ken Welcome Aboard...
First off it's best to start your own Topic even if the issues may be similar...this will ensure it recieves the proper attention.
Now to your questions and we need some more info as well:
An 80 pin IDE connector is the same connection to both the drives and the MBoard...the way to tell them apart is the actual wires in the ribbon are thinner ( there's 80 of them instead of 40)
When you replace major components the system will sometimes hiccup as it's still looking for the old hardware since those are the drivers currently installed.
Repair Install of Win2KRead thru it and get familiar...also print out a copy for reference.
Take your time and follow all the directions.
If done properly you will be back in business and all her data and programs will be intact...if you make a mistake you risk losing everything but you will have a clean install of Win2K
When finished the first thing you need to do is install the new MBoard drivers...they will be on the CD that shipped with the board.
Following that then any other devices such as vid card; printer etc.
Then connect to the web and update and run all your protection apps.
Best of Luck, let us know.