I finally got around to checking my CEL and I had these codes on my 2000 Civic HX:
12, 22, 48, and 80.

The first thing I did was clean out the EGR valve which was completely stuck and the ports were blocked. I cleaned the valve unit itself and the ports on the car itself. This didn't really do anything so I took off and cleaned the EGR plate and cleaned out all the holes under it which were all completely clogged.

All the codes were clear for about 20 miles and then 12 came back and has stayed despite checking the valve several times and checking the plate one more time. All the ports are open and clear and the "pin" in the EGR valve moves with pliers. The only thing I haven't done is change the EGR chamber gasket because it's kind of expensive and seems fine, just rather caked in carbon that I couldn't get off with normal carb cleaner. I suppose I should just spend the $35 and order this part, especially if anyone here says so. I suppose its imperfect condition might be causing an imperfect seal for the EGR chamber and that might cause the code?

It's weird that right after I cleaned the EGR chamber all my codes went away for a decent while but after the one code comes back pretty quick. Coincidence?

Last time I took out the injectors I noticed one of them is missing an o ring. I'm not sure if I lost one the first time I took the gas rail off or if it has always been like that. The engine seems to run just fine with no roughness or misfires that I can notice. I doubt this would cause CEL code 12 but I will replace the o ring anyway because obviously it shouldn't be missing.

I don't know what else to do! I have to renew my tags in two weeks and after a few weeks of messing with it I need a better plan. I'd like to test the EGR valve itself because maybe it needs replacing but it's too expensive a part to replace in the course of trial and error. (I can get an Accord EGR valve for cheap but the wiring faces the wrong way and I'm not confident in my ability to extend the wiring in my car.) I've gleamed from this forum that replacing the computer itself might be an option but that's not something I want to try without conviction. I also have gotten the impression that I could jump some certain connectors to make the ECU ignore EGR problem. The car is running great and I think cleaning the EGR has improved my mileage (I don't have an odometer) and all I need to do is trick the emissions, though I wouldn't mind fixing the actual problem.

Edit: It's a 5-speed, if that matters.

 

I'm thinking I might be able to narrow down my problem to the valve itself and not the chamber because I used to be getting codes 12 and 80 and now only get 12.

12 EGR - exhaust gas recirculation lift valve

I'm going to get it scanned tomorrow or today if I have time so that maybe an actual scanner code will give my specific information. I will remove the EGR valve (for the seventh time) and clean it out again. It would be great if I there was a way I could test the valve itself! Like attach wires to it from the battery directly and see if it moves or something. I don't really know how it's supposed to work but I assume the computer causes the plunger in the valve to move up and down.

 

I hate to bump this pointless thread but I don't see a way to delete it and I don't want anyone to have to waste their time.

I ended up just replacing the EGR valve with one I found very cheap at O'Reily's. It worked great and the code went away. Unfortunately p1259 has come back with a vengeance.