I can't even build your 1.4 source code without any changes, so I'm unsure what to do there.
I just want to say that I'm not an experienced modder, editing the AI is all I did and the Superior AI source files sort of include all my very first mistakes including having lots of useless files around that aren't actually used.
Honestly, the best thing I can say is that you should try to make sure there are no conflictions, they won't resolve themselves it'll just break. In some cases it's best to just leave the files intact but find ways to exclude them from being used in game. You can see this happening in the additionalmaps/common area of the source code in SuperiorAI, where Warren, Lissete, etc aren't actually removed or replaced, they're just redefined here instead. Because it's always better to make your own than to edit an existing AI file or remove. This is the best way to make ra3 AI without crashes.
I should also mention, embedding the AI would take quite a bit of effort. A lot of the stuff you've added wouldn't be used by the AI without being made to. There's also the fact that your mod includes some files that mine does too which means I'd need to know the changes and make sure one file includes both changes. So I apologize and am sorry I don't think I would want to spend so much effort and time into such a task.
JonnyKnows
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