@pfrsantos
Those are the goals.
I had started by modifying an existing theme until I got close to what I wanted it to look like, then decided to create a custom theme instead.
I build the new theme and fought with a few settings, only to realize the old theme mods were still in place. #facepalm.
Currently I am working on removing any duplication between the theme I created and the custom CSS/Header/JS that modifies the theme so I can remove the custom mods and just have the theme.
I am also trying to clean the code and organize the changes so that when we have issues with something five years from now, we will be able to find things quickly and easily.
Once I have all of that stuff sorted out I will come back and start dealing with the smiley box, colors, widths and other visual issues.
The next step after that is to try rebuilding a few modules like the Treasury, and one that allows us to keep using standard BBCode like the [img][/img] tags you have discovered don't work yet. 
And, at some point, there will be the SMF import, but that will probably mean shutting the forum down, pulling a backup, using the importer module specifically designed for SMF and then a whole pile of cleanup and config once that is here.
And at some point, the MTO specific smileys all need to be imported and I doubt they will come with the rest of the import.....