I really suspect that your original remote was defective or that there was something else odd going on - had I heard about that problem when you first encountered it, I would have recommended calling Outlaw at the time, because the remote just "not working" intermittently is not typical. The Harmony remote will resolve it, but there was no reason to suffer for so long. The Zone 2 remote is literally just for Zone 2, however you can change inputs from the front panel - don't despair. Try using the combination of "INPUT" button and the up/down navigation buttons on the front panel. There are several front panel controls that work this way, including the "SURR MODE" button. The button puts you into a sort of "edit" mode and the navigation buttons do the actual changing.

As for the DVI, I still think that was the right choice at the time, and I still chafe at the fact that many receivers and processors released with or even after the 990 include HDMI inputs that offer no audio capability (a fact that is often only discernable by noting the absence of mention of audio over HDMI in the manual, or from a small sentence buried somewhere in the literature identifying the HDMI connections as being for video switching only). Using the DVI connector removed any question about how it was working, and I've used my 990's DVI switching with at least two DVI video sources and six HDMI video sources (eight, if you count a couple different outboard HDMI video switches that I've tried along the way) with consistently good results. If I see any blame to be handed out there, it's to HDMI for releasing an immature spec too soon and with too much uncertainty about where the spec was headed in the future.

As for the firmware update procedure, I find less issue with the need for direct connection to a PC (something that is common on nearly every receiver and processor on the market that offers the ability to do firmware updates) than with the firmware update process itself being a bit cumbersome in some cases (an opinion that I think Outlaw recognizes). It's not convenient to connect to a PC, certainly, but at least you aren't having to drive (or ship) the unit to a service center for the update - as was the case with some recent Onkyo and Integra units that actually had RS232 ports for update but for which Onkyo would not hand firmware updates over to consumers.