Perhaps I was a bit vague. From all my experiences, and Ive seen others mention it too you need to hijack some power from the floppy power connector to power larger drives.
Your choice of the words butcher and hijack are the problem. For a 3.5" drive you need to get power from the floppy connector, however you can get a splitter cable that just plugs in to the motherboard, floppy drive and hard drive. No butchery to the motherboard is required.
You also need to get a 44->40 pin adapter, or use a idefix adapter which usually has a 44 pin socket on.
Compact flash doesn't need to spin up, so is available quicker and doesn't make any noise. It also seeks faster. The transfer rate on hard drives is higher. On a 68000 based Amiga using PIO, it's unlikely to make any difference at all.
