Issue 1 certainly sounds odd. When I read that component monitor out will work but the sources themselves wouldn't appear, my first thought was a resolution incompatibility. The opposite is often true because folks with older HDTV's connect the component monitor out to an input that only supports 480p or higher resolution and the 990's menu won't appear because it is in 480i. In your case, though, I assume that you connected the sources directly to the same input that the 990 was using and got video straight from them without trouble. I'd start by making sure there's nothing wrong with the cables running from source to 990 (reversed cables, loose connections, etc) and then make sure that the DVD input is set to use "COMP-DVD" and the Video1 input is set to use "COMP-VID1" (assuming that those are the two inputs that you connected to on the 990's rear panel).

The second issue is simpler: you need to adjust your crossover settings before running the auto setup. Turn your crossovers down from the 100Hz default and leave them all as small. You might also want to prop the microphone up around ear level in your listening position if you haven't already (I used a little tripod, but even just a box or something will suffice). I think some folks have also set tone defeat to "on" (disabling the bass and treble tone controls).