Whats the Difference - ASP & ASP.NET

Doing bits at a time can get you in quite a mess, it might be better to re-write and release fresh when it's completed.

I've seen people take an engine aproach to upgrading by first redoing common functions into their own application api - e.g. a .net data base engine that you can convert all your existing db ACID stuff to and later a display engine to handle .net output from the db using web controls. etc.

The nice thing about starting with db and display engines is that you can convert scripts at your lesiure - don't have to do them all in one release, or at least you can bundle the conversion to an engine in several releases.

As michael noted, some sort of url handler/rewriter is probably the most important thing in your situation if you plan on reorganizing your site or renaming pages. You don't want to screw up years of search engne placement. I wouldn't do the url handler as my first .net app though... it's to important to the site.