Upgrading Atahualpa and migrating settings and PHP customizations

Hi
I am a gold forum member, but have been out of the loop for awhile.
Hope you can help with this.

I will be updating some of my older WordPress installations with the latest WordPress and Atahualpa , For example I have an installation of WP 2.9.2 and Atahualpa 3.4.6.

I know that I can update my WP site and custom WP settings should be maintained, but how do I do that with Atahualpa and still maintain my custom settings?

I don’t see a way to migrate Atahualpa settings from an older version to a newer on (except for a ‘settings’ export from a newer Atahualpa version that 3.4.6)

There are two areas,
1. the basic settings which can be exported in newer versions of Atahualpa, but not in 3.4.6.
2. The custom changes I've made to the PHP files, like advertising code and other changes like changing headers or footers.

Is there a way to go from an older version to a newer version and bring over the older settings and PHP customizations?

Do I have to copy every single setting manually from the old settings and all the custom PHP files and manually copy the changes back into the new Atahualpa installation in both the settings area and the PHP files are?

Any help would be greatly appreciated.