Dan when is the 2% put into the bonus equation? Is it part of that last large bonus?

no, it actually looks like it's being applied directly to the raw points available from structures, before that number is shown on the production tab just to the left of the full production amount

we have 4x +75 research base structures... that should be 300, but our +38% is making it show as 414

Other Bonuses strictly shows percentage increase from Level, Defender, and Loyalty bonuses

Thanks