I'll start with the most recent and pressing concern, the charging system.
I have been unable to drive the car for some time now, due to in my opinion, its complex charging system. The alternator is controlled by the ECU and the ELD (an integral part of the "under dash fuse box". To make troubleshooting difficult, if not impossible in the driveway, one can do very little testing due primarily to the solid state ECU (do not check for continuity). The alternator has been bench-tested, the battery is new, continuity has been checked in as many harness wires as could be, and of course the fuses are all good.
Just to make it more puzzling, the headlight retractor warning light is on, but the retractor system seems to be fine. I have read about later model Civics with ELD problems, but have not come across anything about Integras with any of these symptoms.
As of now, I am faced with the terrifying option of bringing the car to a dealership $$$$ as I suspect the ECU to be at fault. The factory diagnostic book has a recommendation to substitute "a known good ECU" as a last resort ; high-tech huh! :)
A/C died several years ago. Manny, Moe, and Jack quoted $1,100.00 to replace the whole system because it was "run dry". My understanding of the system is that it has a pressure switch to cut the compressor off if the refrigerant drops too low to prevent it from "running dry". I guess the switch must have failed first.
Water leaks - I thought the sun roof was the problem for some time, but not so. The plastic cowling at the bottom of the windshield has shrunk and distorted allowing water to flow under it and cascade into the fresh air duct. The trunk area was leaking due to a rust spot caused by an unsealed body weld at the hatch opening, and water leaking in around the tail lights.
I did have one good experience with the ECU. It did get me back on the road quickly when the crank angle sensor went out. A specific code and clear step by step diagnostics in the factory books was the key to a quick repair.