I think it's awesome that my work on Bonfire has inspired you to dig a little deeper into some of the CI resources out there, like HMVC.
If I were you, I'd try just inserting the main app into the app folder and start going from there. Once you get it working, you can start refactoring your code into modules. I don't think it would work to drop the code into a module, and would make things harder for you in the long run.
As for performance, my biggest suggestion is don't worry about it too much at this point. For most of the sites that a lot of us create, it really doesn't make a difference. PHP and CI are fast enough to work well for most sites. If you have a site that starts to become popular, then it might matter. Until then, it's best just to pay attention to how you can structure your site to take advantage of caching, if you do anything at all.
For most of the sites that a lot of us create, it really doesn't make a difference. PHP and CI are fast enough to work well for most sites. If you have a site that starts to become popular, then it might matter. Until then, it's best just to pay attention to how you can structure your site to take advantage of caching, if you do anything at all.
