1. Since the newer DTV HD receivers all use HDMI and the 990 only had DVI, do you recommend getting a HDMI to DVI cable or using a HDMI cable (already have) with an HDMI to DVI adapter? Is there a difference in quality?
There's no difference. I've done both (DVI-to-HDMI cable and HDMI cable with HDMI-to-DVI adapter). The only caveat is that I would
not run a DVI cable with a DVI-to-HDMI adapter because of the weight and stress applied to the HDMI connector.
Or would I want to stay with component since that's the way the Direct Tivo is hooked up now and the best connection to my tv would still be component also?
Well, once you change TV's you will no longer have the component-only limitation. In my experience, I've found no difference in picture quality between component or DVI/HDMI with HD cable service. For other sources, though, HDMI may be preferable (Blu-ray, for example, or some DVD players with good upscaling that only works via HDMI).
2. As far as I know most newer Direct TV HD receivers loose the RF out so I need to think of a way to still get that signal to an upstairs bedroom. I'm assuming that all newer HD receivers would still have analog audio and video out am I right in assuming this?
I don't know enough about DirecTV gear to know what outputs they offer, but as a general rule any video source today will still offer some basic "legacy" analog outputs (both audio and video). You may not be able to run RF without adding an RF modulator, but you should still have analog audio and video outputs.
3. If all new HD Sat receivers do still provide both audio and video analog out would they still be active while you would be using either HDMI or component to the 990?
Again, I don't use satellite so I don't know. With cable boxes, you generally can use both outputs at once (although HDMI generally disables component output in my experience). You may have some issues with aspect ratio control - I know that I can archive things from my box's DVR to my DVD recorder with the proper aspect ratio while I watch something else via HDMI, but I don't remember if SD content gets squeezed & pillarboxed at other times. I think it may.
I do have a friend with satellite (not sure what provider) and he has two receivers that share a single DVR - one is an HD unit with the DVR, and the other is an SD unit that can pull recordings from the HD unit's hard drive.
4. Providing answers to 2 & 3 are yes, would there be any issues running analog cables A/V 50ft to 75ft to the upstairs bedroom? I see Monoprice has cables pretty long for a decent price.
You have to be a little careful about runs that long and possible interference (being parallel to power wiring, for example). It can be done, though. If you already have the coax cable run up there, though, you could also just get an RF modulator from Radio Shack for $30 and connect the AV cables to that.