If you can arm the tracks on the HDR from the D8B, then the MIDI communication is working. So, that would indeed mean that something else doesn't work with the transport control buttons. You'd have to open up the console and take a look. Is the red SMPTE display still showing something? (Just wondering if that section/board is getting power). Anyway... to fix it, you'll have to take a look inside first.
Yeah, the problem with the channels that don't work right, I'm not sure about. Sounds like the faders are "bypassed" somehow and don't do anything. Not sure if that means that the faders would need to be replaced, or if something like a leaking capacitor that's responsible for it (or something similar) could cause a problem like that. Hopefully, someone else on here has an idea.
The "clicking" I meant, was "digital artifacts" from not having the desk synced right. If it's clicking when moving the faders, that's also something else. Sounds a bit odd, though... so, will there be a click in the recording when moving a fader? Or is it on the output of the same channel where you're moving the fader? Or is it just some mechanical noise, that doesn't make it to the audio inside the desk (in that case, I'd ignore it).
About using the internal Aux effects... it's a bit confusing at first, but technically works the same way as when using external effects. I think what I got confused about when using this first, is that I had to select in the plug-in window, what Aux channels the signal comes from, and where the signal is returned to. I don't have the desk on right now... but if you choose the ins and outs of each plug-in correctly, then they should work the same way as when sending signals to an external fx unit.
Anyway - sounds like you have everything in a condition that allows you to work on the demo! As for the other stuff, I can try to help, but in that case, let's do this one issue at a time... but then I'd need more details for that one first issue you'd like to takle
