Thanks for kind words CB! And the help debugging
Actually the gun thing is not a bug. This should be on the research card, but maybe it is not that obvious (it is in the manual), but the 30 mm guns don't go with Light Tank II, but are required for either Light Tank III or Medium Tank I. In addition, once you have researched the gun, you need to "improve" the model in the model designer. The manual shows the matrix for guns and models. Note that Medium Tank I will only tank up to the 50 mm gun. When you research the 75 mm guns, you need to research medium Tank II and make a new Medium Tank model. Your MT I model is essentially obsolete. You cannot upgrade the model to MT II (but you can upgrade the SFTypes that are in the units). Tonight, I'll copy it and post. The same goes for the armor improvements, after you have researched the tech, you need to "improve" existing models. New models, however, will have improvements automatically applied to them. Some techs, however, lead to an alteration. For these, you need to actually apply the alteration before producing the model (this is an ATG rule).
As for being different than the base model. There are two reasons for this. First of all, the base models are ONLY available to the AI if models are used. The AI can't use models, and the AI wouldn't really know what to do with the guns. The base model represents an average of what you can get with the model system. So, the models you start with will not be as good as the base, but if you keep up the improvements, your models will actually be much better! To compensate for the improvements, I did make the techs a little cheaper for human players to help balance things a bit since you will go through many more models. On the other hand, in general the AI is beatable, so this is one little advantage it gets that can help balance it out.
The other thing is that the models are not monolithic. There is a bit of variation (just as in ANewDawn). Some models will be just a bit different with the same tech. It isn't huge, but it is for variability. And, well some models are just better. I am pretty sure Patton might have preferred some PzKpfw IV or V instead of the Shermans, but that is what he had to work with. It would be help create General envy between human players.
There is one small quirk with the models that is rather minor. If you research Level N+1, you will still the Level N model concept is still available when you go straight to the model builder. This is a quirk that you can't make a model obsolete with a setting. It will, however, become unavailable as soon as you make a Level N+1 model. It will disappear from the list. This is by design. The models have a secondary tech that is required, and I take that tech away for the Level N model when you make a Level N+1 model. Just can't do it in a simple way that makes it so that you never see the two of them together.
HQs, that's OK. For the most part though, the AI tends to have several units assigned to them, so they get wasted. Also, the radius is about 3 hexes, which more or less lets them support 6-9 units. You might want to consider keeping the HQs in roughly every third city as armies and assign the corps to them. I think this can be done.