Ok, here's a quick & dirty explanation of what the AI is doing and why it won't do what you want... the key to your problem is
'...the aircraft assembly plants are basically copies of the factory building. The difference is that I had to reduce the number of hammers generated by all factory type buildings...'
When evaluating what to build the AI defines a value of each building based on what the building provides as bonuses, so if it provides no bonus the AI won't build it, ever. Pretty slick really, and it works very well as you can see by making two buildings that are nearly identical with one have some extra bonus, the AI will always build the one with the extra bonus first.