Impressive work! 
You really outdid yourself! 
Fixing the campaigns is still on my to-do list. I had a look at it recently and noticed, that the fixed scenario-files won't work in the mod-folder. Having to overwrite the originals wasn't something I was keen on doing. Your method is quite an interesting workaround. Not to mention quite obvious, once you think about it. I really miss the forest for the trees sometimes.
Two things I noticed:
In the first mission of the DL campaign, the Terrans don't have access to Advanced Starbase Construction. This means, that they can't research Starbase Fortifications and onwards, even though it is available. I haven't checked if that is also the case with the other missions.
1pp upgrading to 1pp. I used this myself before, but noticed a pretty serious bug. The game counts the upgrade as a second building. So, if the improvement gets destroyed, you won't be able to rebuilt it. Same goes for the AI. This bug is easy to overlook in the vanilla game, as there are only two series of 1pps that can be upgraded (Navigation Center and Power Plants). However, if you disable tech-trading and -stealing, and play with the right combination of races (like Arceans vs Drengin), you will notice it.
Some clarifications:
Star Federation provides a 40% bonus to economics, not 30% like the description states. So, it is actually much better than Star Democracy.
The way minor races loose access to technologies is actually quite simply. It all depends on if a tech is unique among the major races or not. For example, in a match between the Arceans and the Drengin, Planetary Improvements is only available to the Arceans. So, the minor races will loose access to it. The same goes for all the other techs, that are only available to one of the majors. The type of the tech doesn't matter.
For nostalgic reasons, I had a look through the old Dev Journals last November and found out the reason behind this behaviour. During the early beta of TotA, the minor races had no tech tree of their own. Instead, they had access to all techs in the game. This means, that the minors could build the Shrine of the Mithrilar, and other improvements unique to certain races. The players didn't like that at all, and the Devs finally implemented this tech-limiting behaviour. At the end of the beta, the minors got their own tech tree. The tech-limitation, however, remained. Probably because it got forgotten.
Well, I hope that explains it.
