How to manage a large empire toward end game?

[paplan]

Hi--I'm at the late-middle end of an SE IV gold, TDM3.40 game vs the computer. I started with 12 races, and now there's 5 left; the Klingons and I are on top. The hard part is all of the tedious stuff in managing 70+ planets and 100s of ships. I'm using waypoints to bring my new ships to the "front", but the front keeps on shifting by the time the ships are built. Also, I spend lots of time sending my carriers back for more fighters, and repairing damaged ships, designing ships, and updating ships, etc. Any tips on how to make things simpler? Are the minsters effective for these tasks?
Thanks