I just finally broke down to clean EGR Port. Disconnect all vacuum hoses, water hoses and electrical to top plenum. Plenum is connected to throttle body and top of intake mfld. The hardest part was getting the water hose disconnected on the back side of plenum. Car has about 200K miles and hoses were very tight and hard to remove. I used needle nose pliers and flathead screwdriver to ease off old hoses. I would get new vacuum hoses ahead of time so you could just change out while doing this job. Remove the plenum and trottle body together from intake mfld.
Remove EGR Valve and inspect ports. Mine were partly plugged. Take EGR valve and bench test electrical while off engine. Check Ohms on top plugs, from 1&2 and 1&3. Bottom 2 are numbered 4 and 6 looking at plug 4 on left. You can test valve with #4 to positive battery and then #6 to neg ground. Valve should open when connected. Open and close several times to check. The top pins #1,#2,#3 should read low ohms 1-4 between them and will vary as the different amount of valve position is opened or closed. Shop manual has details. If electrical test pass, soak valve portion in carb cleaner while working on EGR ports on engine.
Dissolve EGR port with carb cleaner; I did not have a cleaning brush, late last night, so I cut a heavy coat hanger wire and bent to push through port. Round cleaning brushes would be great to have for this. Gun cleaning brushes should work also. Soaked EGR port from top of plenum down to the EGR location and from EGR back to engine with cleaner. I filled ports up. Scraped inside of ports to remove loosened deposits then used hand vacuum pump to suck cleaner back out. Repeated soaking, scrubbing and removing with vacuum pump until cleaner was not dirty looking. Of course I plugged hose several times with carbon while removing liquid. I did this 3 times. Also inserted cloth rag into port to absorb remaining cleaner.
Once all liquid absorbed and removed and DRY; I used a wet/dry shop vac to pull any remaining carbon and small drops of liquid out. DANGER BEWARE DO NOT vacuum LIQUID with shop vac as a fire could occur with vapors and electrical sparks from the vacuum motor. That is why you use the hand vacuum pump to remove most of liquid. Course you could use compressed air to blow out, but would make mess all over engine and yourself unless you cover port with rags.
So I dried out best I could with no visible liquid cleaner showing up on paper towel. (Be careful putting paper into ports and falling apart inside the port when trying to remove while soaked with liquid. I learned the hard way and it took extra time to remove pieces of wet paper.) So use cloth rags first to absorb most of liquid and then paper 2nd to absorb the remaining residue, then shop/vac or air.
Since there is only 1 EGR port on this engine, it is easy to get to and clean. No boring out of plugs etc.like older cars. I did not remove intake mfld from engine to clean this. This took me about 3 hrs to clean and put back together. Cleaning took about 30 min with soaking, scrubbing. This was first time doing this so I was not familiar with job. Next time, hope I never have to, should take only half of time. Reset the engine light and you should have no EGR codes now.
Problems: Could not get new plenum gasket at local Autozone, O'Riely's, Honda shop closed, after 7pm. They would have to order. Removing water hose on back side of plenum was not easy.
Solution: Get plenum gasket and new EGR gasket ahead of time. Get new vacuum hoses so you can cut to length, assorted round wire brushes to insert in port to clean, cheap plastic brush bristles will melt with cleaner but may last long enough for this job. 2 cans of Carb Cleaner, hand vacuum pump like you use for brake jobs or a vacuum bulb to remove liquid, compressed air in a can if you do not have air compressor.
Do Not buy new EGR valve unless you have verified you ports are cleaned and tests on EGR valve with engine running indicate valve not opening. They normally are not the problem.
Hope this information helps remove the EGR Codes.
Some photos of before and after opening intake plenum in Photo Album. EGR port was plugged solid.
See link: http://honda-tech.com/members/vinnyg-999762556-albums-honda-accord-99-egr-cleaning-35260/