Now....what HTML are you talking about?
Any aspx page is has a .aspx file and a .cs file. The cs file is your code behind, the aspx file is your page, containing all your HTML, including the asp: tags that denote controls. When you're in the form designer, at the bottom of the page is a 'html' tab, if you click on it, you can hand edit the files. This is definately the way to go, and you should set up your preferences to always go here instead of the designer, for the reasons I mentioned.
And if it were me, I'd create a new control in a project, then copy and paste the html and C# code into it, then change the namespace of the class to match the project, and try to use the control in a page. Unless it's a server control, that's just a cs file, but I'd do the same with that. Not least is the fact that you could then set break points and step through the constructors, etc. to figure out what is going wrong.
I have drunk the cool-aid and found it wan and bitter. - Chris Maunder