Well, Miharu is running very hot due to the coolant having been reduced to 70% of normal. The three remaining CFS units are already past tolerance - more use of them and they'll probably be melted enough for BAD THING TO HAPPEN(TM). Yukari chose to shut them down and rely on the single gravimetric engine they have left. Regenerative shields are also presently down by Yukari's choice.
The energized armor is toast. Too much of the ship's outer armor took damage for it to function adequately anymore.
Main engineering probably looks like a mess with all the scorchmarks and weapon fire that's been flying around, but the rugged equipment there actually held up pretty well aside from the hyperspace fold drive, whom was destroyed when a Mindy invader decided it'd be fun to gut it open with an aether sword.
The entire port wingpod is a wreck. Nothing works there anymore and the whole gravimetric fin was severed due to the damage there. The nearby lower fin that held damage control and an escape pod-turned-fusion reactor suffered a meltdown and exploded... meaning that lower winglet isn't there anymore. There was a coolant leak that Junko, Tom and Ichigo were tending at the stern-end of the port capacitor maintenance accessway. Shortly after they were done, there was a structural collapse that nearly killed Tom; Junko sacrificed herself to protect him.
The port capacitors still work, and they've got enough charge for 3 main gun shots.
The starboard side of the ship is faring okay for now. The capacitors there were depleted of energy due to a nearby positron strike, but none of the equipment there is too badly damaged.
Note that with the loss of an aether generator, Miharu's main power was reduced to 75%. There are still three fusion reactors left to help pick up some of the slack (especially considering how they were designed to fuel the energized armor... and that that system doesn't work anymore).
Miharu's structural integrity estimate is presently around 40% after the latest decompression. The way the structure of the ship is feeling (from the sounds and vibrations it emits when under stress), it probably won't be long before some very nasty structural breakdowns happen.