Interesting idea. I'm 3 years into a game with major-minors and things seem to be going well. Other than the minors, the game itself is pretty unremarkable, making it hard to do a write-up. I do have some experiences and observations that might help you, though.
1) Minors can, in fact, become pretty powerful.
I gave all my minors some bonuses to make them competitive and reflect their descriptions. Of course, I also changed their descriptions from the drivel they came with to something respectable. While trying to be balanced, I decided to try making a monster just to see if I could, giving the Dark Yor some pretty hefty bonuses to economy, morale, pop. growth, and production. It worked. While the other minors have from 2 to 7 colonies, The DY are keeping up with the majors and have 32. Actually, I declared a preemptive war against them to slow their expansion. If I hadn't been destroying literally dozens of their colony ships over the past 2 years, they would probably own half the galaxy.
So far, I can't say anything about their military. For whatever reason, the AI hasn't switched from colony-rush to war, even though I've been pillaging both DY and Torian space for years. I can just say that with the right bonuses they'll do just fine and with balanced bonuses they'll remain pretty minor powers.
2) Minors start with only 1b population, so your Yor and Thalans will have an inherent disadvantage. Their economy and expansion will be slowed compared to the majors. It's possible to compensate with economy or pop. growth bonuses, but those will carry on past the initial stages.
3) I'm not sure if you can change the starting system/planet for minors. Sure, you may be able to input the custom system for the Yor and Thalans, but you may just end up with the system name and typical PQ15 planets for minors. Would like to know how it works out.
4) Minors are not only immune to influence, they also project no influence. Anything relying on that won't work. e.g. the weapon and defense techs that give bonus in your influence, and the Super Isolationist speed restriction.
That's it right off the cuff. Let us know how it turns out, even if you don't do a full AAR.