I've used JSON for config files, that way you can basically code the AI and toolkit in objects and the config format looks after itself. You may find that easier if you are going to rewrite the toolkit...

The configuration format will eventually be lua. Im thinking more though as to what the UI will look like, atm the tabs full of arbitrary options thing isnt the best idea...

what about generating something that looks a bit like the mod info site:-

http://modinfo.adune.nl/index.php?act=e ... &MOD=ba691

you could then put the options on each unit - might be a more intuitive way to lay it out