At the end of the instructions, it says you must consider any modifications you've made to the CMS and "remake" them in the new version.

They can't say exactly *how* because they have no idea what you may have done to the CMS. Putting code in the App_Code folder is a pretty standard thing to do, but it's also pretty easy to bring into your upgraded version. Just copy the code you put into the last version back into this new version.

While you're developing custom code within a pre-built app, it's good to keep these issues in mind so when upgrade time comes, you know what you need to do. That's why it's good practice to keep all your custom code in a #SITECODENAME# folder within the App_Code folder. Then its as simple as copying that folder back in after upgrading.

If you've made other modifications (for example, to the CMS Desk itself), it gets more complicated, and that's when its good to keep up-to-date documentation of your changes, both for your own reference, and anyone else who may inherit your code.

It's also good to have a decent file comparison utility in your toolbelt. I use DiffMerge (http://en.wikipedia.org/wiki/DiffMerge) because it works well and it's free.

Hope this helps,
Elijah