Let me get this straight...you looped the click because because you were monitoring through the amp and not the computer, right? Was there any way to monitor with headphones from the computer, so you could listen to the click out of pro tools? I guess thats what I'm confused about, why the need to reloop the click into the amp instead of listening direct from the computer? You always want to monitor from the last place the audio hits or from wherever its being recorded i.e. "from tape". Of course there's exceptions if you're doing a cue mix or something but thats opening a whole other can of worms.
Another thing, was there two different CD inputs? You said you put the click back in "again in CD LINE". So were you still running the mixer in through another CD input? IF so, thats wierd, I don't think i've seen two different CD inputs. Different phono inputs i've seen (my amp has three!!)
but not CD inputs. IF that was the case then thats definitely what did it, you fried something with two pretty hot signals.
If it was just one input, we're still right, the signal was too hot for a consumer line amp. Either a high end/hifi amp (which you don't really need hifi in this case) or a workhorse monitor amp like a JBL or Peavey or something is what you need. The latter of course will be much cheaper than the former.
As far as what precisely is wrong in the amp, I'll leave that up to Peacefrog, it sounds like he knows much more than I do about that stuff. You know, Parrish is a wizard at amp repair, or audio repair in general for that matter. If you know him he's really the guy to ask.
"Is this what you want you want to do with your life, man? Suck down peppermint schnapps and try to call Morocco at 2 in the morning?"