Just a few thoughts in response...
I did test the Jet Inst fx as I remember someone mentioned it a while back and it appeared to have 100% fade?? Didn't test any others though.
Sidechain vol's appeared to be OK to me, although I was only using headphones (sleeping baby). Didn't test the noise fx. The new sidechain fx are sweet, I like the manual trigger option too.
I think it is only very loud if you have the output channel volume turned up while recording because effectively the same track is being played on two channels perfectly in sync. Once recording is finished it starts looping and the output channel is no longer playing the exact same sound as the source channel. Although I haven't tested that theory yet. I think if you turn the output channel volume down when recording this should avoid the problem.
4. I only found that it would go out of beat if I modified the pitch on the CDJ... when I did this the mixer would add or remove sound from the end of sample. So effectively the sample would still go for 4 or 8 beats at the new BPM but the mixer does not stretch or shrink the sample, therefore the beats no longer match up. I found if I left the CDJ pitch where it was when I took the recording I didn't have a problem using the channel as the BPM source. Even when I changed the pitch then moved it back to its initial position it would snap back in time at the next loop.
+1 for the thumbs up!