I would start by marking all my cables so you know where to put things back and then pull it all apart. (If you have changed setting in your TV and/or receiver as much of a pain as it is I would go to every menu and lable the menu and each setting in it and what it is set to.
Now, reset your TV to factory. Pick you poision as where to start, but the combinations are feeds to TV first, no other crap in the mix.
If you have a HD DVD it should play SD discs also. Start with an HD disc and say either an HDMI or Component connection to the TV, see if it works. If it does it means that there is likely nothing wrong with the input channel you used on your TV or the output on your HD DVD.
Then pull that out, using the same imput to your TV if possible hook up your Direct TV. First, check with Direct TV and make sure you don't have some package where you don't get 480i stations, like some funky HD only option although I have never heard of it.
Test your Direct TV on HD material and SD material, if it works then you know again that input on your TV is OK and you Direct TV is OK.
I am sure you get the idea from this, take it one thing at a time, one set of cables at a time, the same ones if possible. On the Cables, if you can test them with each thing you found working, then test the next set of cables, this way you can eliminate a bad set of cables if you have one.
Then add in the receiver to the mix, and repeat the same steps. You need to isolate what is not working and that will likely either be common to all things not working, or introducing the issue to all other things even if they don't seem related.
The last problem I worked on like this was for a friend, it turned out it was is HT receiver that was the guilty party, and he had everything running though it, as long as the HDMI cable from the HT receiver was plugged in to the TV, things were not right even when the input source was from something else, I have no idea why.
I don't have enough info to tell but it sounds like your TV or receiver, this is why you need to get the receiver out of the mix and find of anything works right on your TV from some source, even if you have to trage out an old SD DVD or VCR and use the simplest connection to the TV possilbe, composite running a 480i connection.
You have a lot of variables, what you need to do is start eliminating the variables, cables, signal resolution, TV, Direct TB Box, receiver, Wii, etc...
I know this sounds like a pain but until you get it down to one thing at a time to known working things, then you will just go in circles.