I don't think you have done all I'm telling you or it would work.
The main criteria are that the variation (repaint) is installed correctly (selectable as a new variation from the FS2002 menu) & the AI database is correctly updated with TTools. If not, it can't possibly work as AI traffic. This needs doing carefully as a small typo can mess it all up.
I don't know of any limit to the number of variations you can use. If there is a limit it's certainly more than 3 for each aircraft. My Add a Repaint walkthrough is only basic & you can change the ATC entries for the different variations in Aircraft.cfg later if you wish. The older FS2002 version of TTools should be fine but it wouldn't hurt to use the latest version. This is a little more user-friendly & compatible with both FS9 & FS2002.
http://www.simviation.com/fs2004utilities1.htmMake sure you read the instructions carefully & understand how it works.