I have 3.4.4 installed and I have made a lot of customizations and looking to upgrade.
Is there a post or thread already on the best way to do so?

The options you set via the theme options are stored in the database amd will carry over during an up[grade. If you made any changes to the code, you will have to redo those changes. I suggest you install atahyualpa 3.5.1 in it's own folder so you can swap back and forth between teh two versions.