PROTIP: Don`t do your missions until you have the planets you want WITH 2500+ loyalty from fighting. Missions grant you 900 total bonus loyalty. That way you can have 3,400 loyalty, that`ll be the best possible thing to do for your income.
When clustering planets, loyalty averages out, so if you have 4 colonies with 50 loyalty then another with 2,500, you`d have 540 loyalty after clustering. A way to get around that: Kill all the population on all the planets that don`t have the loyalty. If a colony is dead (has no population) it`s exempt from the loyalty averaging, so that way you can keep the 2,500 loyalty.
If you have any questions feel free to ask.