Not enough info to be sure of what the next steps should be, but did you check and adjust if necessary any BIOS options relating to that old disk?
For example, if the BIOS didn't auto-detect drive geometry correctly (heads/cylinders/sectors) - and set exactly the same geometry parameters as on the original motherboard, then the partition is set wrong and it doesn't recognize the format - and what you would see is the operating system showing you a blank disk and asking if you wanted to format it. Which is what you describe. Making changes to the old disk (formatting, writing files to it, etc.) can result in lost data, so avoid that unless all hope is gone.
The BIOS needs to be set correctly before going much further. If you're certain (or as certain as you can be) that the drive settings are correct in the BIOS, then I'd just disconnect the new drive (to protect it from data loss), disconnect the old drive, set it as master, and connect it to the port where the new drive was. Check BIOS, save changes, reboot if changes were made, and see if it tries to load the operating system that was on the old drive. If it does get this far, it'll puke up a bunch of errors (because none of the new motherboard drivers or disk controller drivers are installed on the old drive). But that's ok because if you see all that, then your data is probably intact and you just need to re-combobulate your system. :)
So, if you get that far.. disconnect old drive, leave as master and connect it to the *other* (Secondary) PATA port on your motherboard... where your CD/DVD is possibly connected to now. Set the CD/DVD as slave to the old drive's Master (on Secondary controller or controller #2). Plug in the new drive back to it's original port and at the same settings (Master on PATA Primary controller 1, most likely). Recheck the BIOS, save changes, and restart... and hopefully you have drive c: (new drive), drive d: (old drive) and drive e: (CD or DVD drive).
Hope this helps. Bottom line is that if your system sees a drive D: now, then it's likely recoverable - and likely just an issue with BIOS configuration of the drive's geometry.
If that doesn't let you recover everything, and your certain (or as certain as possible) the old drive's settings in the BIOS are accurate, then you can use data recover tools, like this:http://www.cgsecurity.org/wiki/TestDisk
to see what you can get back. It works well - but you can also lose data with any recovery tool, and they tend to be targetted towards technicians and not very user-friendly, so go slow/careful and you get stuff back. Like I did last month when a process I ran deleted my program files folder...