I am assuming the previous OS was loaded on the the smaller hard drive?

I would use 'fdisk' to set the new drive active and see if it boots properly. Make sure you have the boot floppy handy, because you will need it to restore back to the oroiginal drive should it not work. The boot floppy must have 'fdisk' on it.

the 'boot.ini' controls the multiboot options. Other system files need to be at the root in order for the new hard drive to boot properly. Those are likly to control the results you get.