I think you're on track! Yes, the OTA tuner and Oppo 970 DVD player should have component video cables connected to the 990, the Tivo should have s-video to the 990, and the VCR should have composite to the 990. Lastly, a component video cable from the 990 to the TV will get you set up.

The digital inputs are completely assignable (as are the component inputs, for that matter) - you can connect the Tivo to optical1, the OTA tuner to optical2, and the DVD to optical3 and then just assign optical1 to Video1, optical2 to Video2, and optical3 to DVD. Then you can also run analog audio from the VCR to the same input that you ran the VCR's video cable to. If you ever use the TV's internal tuner, you'll want to run analog audio from it to an input on the 990 (and this can be either a video input or an audio input like AUX or TAPE since you don't have to do any video switching).

You probably used the OTA tuner's analog audio and composite video to go to the VCR for recording, if I had to guess. You can still do some of that if you want/need to, and we can help figure out the easiest way to set it up if you do. If you're feeling overwhelmed, the delay while you wait for the optical cables can help to get all your ducks in a row (as my wife would say) - it's intimidating, but once you break it down to what you really need and ignore all the extra connections you won't need it actually gets manageable pretty quickly.