Jason,

When you compiled your application to run 'stand alone', I assume you had
a main program or main form that launched when the application started? (The form or program shown in BOLD in the project manager starts first).

If so, place the name of the program or form in the run event. Thats all there is to it. You don't need a menu in your app, although when you decide to make one it will be merged into IE's native menu (KB Q182580)

It also sounds like you may have subclassed the activedoc and called itself from within itself (recursion). That explains the too many variables.
Just stick with launching a main form from the ActiveDoc run method. You will have to build some way to launch your other forms from there. This is true for ActiveDoc or not.

HTH and Good Luck,
Ed