[Azselendor]

I would decommission ships, shut down colonization and go micromanage systems a handful at a time. About 6 or 8 systems tops. Basically I'll dismantle everything in the systems I don't need and automate them so I don't need to visit them again.

Also, I can suggest building a large number of warp-point closing/opening ships and reconstructing the way your warp points are laid out. This way traffic can be funneled along 3 or 4 main routes allowing effective fleet movement.