I suspect the crux of your problem is just simply speed.
I tend to faux my games by testing my nation on the MP map we are going to use with the same number of nations. Usually in a true MP game my expansion is about half of what it is against the AI. That's just how much better real players are at expansion.
While I can laze away several turns with broad based research against the AI, against real people I need to focus on specific targets.
Sounds like you have a better handle on the late game than I do, so I'll not give advice there
