William,
I own the same 94-txh receiver. When the MCACC program asks you to turn up the volume on the sub, it is in fact referring to the volume level control on the actual subwoofer. I had to turn mine up a few times before MCACC could recognize sound coming from the sub. Make sure you have the sub plugged into the proper subwoofer output on the receiver, and you have told the receiver that you have a sub via the setup menu.
The receiver should also convert your component video to the HDMI output cable going to your television. I have a combination of components using HDMI and component video connections, and only a single HDMI cable running to my TV with no issues. My HD cable box and SD-DVD recorder are using component video and digital audio (one is coaxial, the other optical), while my BluRay player and upconverting Oppo SD-DVD universal player are HDMI. Make sure you have all the inputs assigned properly for each component via the receiver's setup menu.