How to manage a large empire toward end game?

[tesco samoa]

use repeat for orders...

With large empires i suggest you use build ques and set up a bunch of them...

for the fighter problem

Build a couple of large transports and have them on repeat going to the planet building the fighters ( which you have on repeat building as many fighters per turn as possible )
loading the fighters and travelling to another planet and drop them off.
Have this planet set up as a waypoint
have the shipyards that are building the carriers set to this waypoint.

that will clear that up

I also recommend that since your sending ships to this waypoint planet... that you just have all your ships go there.
put training facilities on there and have that planet build base yards. have them build fighters as well