I'm not sure with any real certainty that you've damaged the boards IDE controller, but the fact it no longer boots the drive that it used to is a pretty good indicator. Which custom chip handles the IDE on an Amiga 600? You might need to replace it. Though surface mounted chips are really hard to replace. AmigaKit sell A600 MoBos for around $40. I also see them come up on eBay fairly frequently.
Just go over everything slowly and make sure you have the old drive hooked up the way it was before you installed the CF card. You said you had a 3.5" HD in there? How are you powering the 3.5" HD? Did you reconnect the power to the 3.5" HD? That's a mistake I used to make all the time. I'd put a 3.5" HD on my A1200, then freak out that it wasn't working only to find that I hadn't connected any power to it.