Is the adapter you ordered and the 'cable that hooked the HD to the Amiga....' you refer to the same thing?
If so, it sounds like you've got an adapter that enables you to connect a 3.5" HD to the Amiga - hence the additional power connector. You can of course still use the adapter/cable to hook a 2.5" HD to your PC (as I've done myself) - just make sure you've got the connections the right way around. On my adapter (Belkin), the 40-pin male connector had the full 40 pins. More often than not, the IDE cable will have one of the holes blanked off as a key (can't remember off-hand which one). I simply bent the respective pin up on the adapter to get the cable to connect.
Regarding the boot issue, ensure you've set your boot hard drive to master and not cable select. Also ensure that the 2.5" drive is on your secondary IDE and that the bios has correctly identified it. If you still can't boot, try disabling the secondary IDE in Windows first, then attach the 2.5" drive, boot into windows and enable the IDE. Windows should then find the drive and you should then (hopefully) be able to drag your data around.
