I couldn't access the link in your original post to look at anything. Yes, IE is the worst, but unfortunately anywhere from 65-85% of people are using IE for their browser, so we are stuck dealing with it. :(
My recommendation for a place to start is to use either Firefox Firebug (which probably won't help in this case) or an IE developer toolbar so you can view the html and the applied css class cascade that is happening. I'm actually liking the IE8 built-in developer tools as much as Firebug in Firefox. Just wish they'd clear up all the issues once and for all, they certainly have the manpower and the funds to have done so years and years ago! Although I'm already noticing small quirks in IE8 that don't render properly where it did in IE5-7 using xhtml... *rolling eyes*
Anyway, that's a place to start looking at your structure and figuring out what's going on.
It may be easier to put together your own html structure first, and then one by one add the skin objects for DNN that handle the logo, the menu, login/register, content panes, etc. I've done that before when a "conversion" was not working out well or just didn't mesh at all, just start from scratch and get the framework working before plugging in the dnn code, and review the default.css in the portal directory for classes you should use in your skin.css file. DNN can be frustrating at first, but you'll get the hang of it. The DNN 4 documentation can be helpful, too, though it is way way outdated...