My math is off.

[Xazur]

Your ego increases through PROGRESSION, this can be either by exp(limited), pursuits, weapon skill level. You must try to do a mix of them to increase ego fast.
http://gamocial.com/xbox/defiance-le...aise-ego-fast/

[DarknessEyes PT]

I took quite a bit of time to finish my main mission. There really is no hurry to finish it all. I think I was around 1600 or so ego when I did the final boss.

I did make sure to do all the side missions before doing the last main mission, since I heard rumors that if you finish the main story, the side missions will disappear. But I don't know if that is true or not, but I got them all done and then finish the main.

No true.
Side missions temporally disappear only if you replay your main mission.