My 1999 Accord started having major problems with the transmission, so I pulled it out of the car and started getting quotes for a rebuild. For reputable shops the price was around $2,000! Just for the rebuild, not including the labor of replacing it in the car. I couldn't see spending $2,000 for a rebuild that might or might not be done right, so I decided to do it myself. Here is a description of what I did and some references to helpful information I found online about the project. I took pictures of EVERYTHING as I worked, in case there was any question of how something was supposed to be when putting it back together. I also put all the parts from all of the components in Ziplock bags and labeled which component it was from. All parts were cleaned in a solvent tank and rinsed off with WD-40, then Ziplocked if possible. All parts were coated in ATF prior to reassembly, and the friction plates were soaked in ATF overnight prior to installation.
I obtained the diagnosis and overhaul manual from http://www.drivetrain.com/ for $40 (they carry the parts as well). I obtained the overhaul parts from http://www.transmissionpartsusa.com/ for $270 including the Bench Buddy valve polishing tools. I made sure I got the complete overhaul kit, including the steel clutch plates (which turned out to be a very good decision!). I obtained a rebuilt torque converter from a local shop in Los Angeles for $85. After it was finished, I decided to use Redline D4 synthetic transmission fluid instead of the Honda fluid ($150 for 3 gallons!). I also installed a second transmission cooler after the stock cooler (free from a neighbor), and a magnefine filter after the second cooler (http://magnefinefilters.com) ($16).

HONDA: 1999: ACCORD: 3.0L V6. ACCORD: 3.0L V6: Transmission-Automatic: Clutch Plate Pack: Dipstick / Tube: Drain Plug: Extension Housing Seal: Filter: Fluid Pump Seal: Input Shaft Seal. Shift Improvement Kit: Shift Shaft Repair. Performance Parts for 1999 Honda Accord. Aftermarket performance parts are designed, tested, and manufactured to higher tolerances and are required to meet higher performance parameters. Remember to soak all of your clutches in transmission fluid for thirty minutes before you install them. This rebuild box kit fits the following applications: Honda. Accord DX, 2.3L, 1998-2002; Accord EX, 2.3L, 1998-2002; Accord LX, 2.3L, 1998-2002; Accord SE, 2.3L, 2000-2002; Accord.

This video has some very helpful pointers on the B7XA transmission:
http://www.youtube.com/watch?v=nuv9UZumqWI&feature=related
This is a good post on the design of the B7XA, describing the design and issues with it:
http://www.driveaccord.net/forums/archive/index.php/t-2025.html
Anyone who has one of these Accords or Odysseys ('99-'02) probably knows about the problems with this transmission. The design was bad, and they fail prematurely. I have read that one of the reasons for this is that previous generations of Honda transmissions shifted hard and people were complaining about it, so to smooth out the shifting Honda designed these transmissions so that when they shift, the transmission partially engages the gear that it is shifting to, while the gear that it is shifting from is still partially engaged. This results in a smoother shift, at the expense of severe wear on the clutch packs. I have not confirmed this, but it makes sense. I might have more on this in the future, I will try and confirm it and possibly find a way to lock it out so it can only engage one gear at a time. In addition to this behavior, there is no replaceable filter element. The filter is located inside the transmission and cannot be changed without disassembling the entire transmission. There are some other issues I found, such as valves getting stuck due to particles and contamination.

The pressurized fluid to engage the clutches is delivered through the holes in the tops of the shafts. I did not have the tool to hold the main shaft for removing the nuts on the shafts, so I engaged the parking brake pawl and applied shop air to the top of the main shaft to engage the clutches on that shaft and remove the nut on the secondary shaft, then apply shop air to the secondary shaft to remove the nut on the main shaft. I had a friend hold a tire inflator to the hole on top of the shafts while I wrenched on the nuts. When I put it back together I used the same method to hold the shafts on installation. Note that I bolted it to the bench for most of this process to hold it in place.
There are protrusions on the housing that I was able to pry to separate the housing (sorry, no pictures). Note the black filter in the back of the second picture. Yep, you have to take it apart this far to change it!

Note that I had to replace the needle bearing on the top of the secondary shaft. When I disassembled it and tried to remove that bearing it came apart and the needles came out of the holder. That was the only bearing I had to replace. All the other ones looked good on visual inspection.

Now we get to the real problem. The 3rd gear clutch pack. The picture above shows the exposed friction plate. Note that there is no friction material material, just steel. The splines on the plates were blue, and basically fused to the inner splines. I had to pry the friction plates off. It looks like they had heated up to the point where they softened and expanded. There was some minor wear on the outer housing that I had to clean up prior to reassembly.
The 2nd gear clutch pack was getting fairly worn. Some of the friction plates had bare metal showing.
The steel plates for the clutch packs came in a package with no labeling. I had to mic the old plates and the new ones to sort them out and which plates go in which clutch pack. It's a good thing I kept all of the steel & friction plates together and labeled which clutch they came out of... The friction plates appeared to be all the same, even though the friction pattern on the old plates varied for each clutch. The kit that I purchased had the same number of plates as the original, but the Honda parts stores show a different number of plates in the clutches. I think they might have changed the design and made them thicker with fewer plates. Not sure.
Note that the manual calls for measuring the clearance between the clutch end plate and top disc using a dial indicator. I do not have a dial indicator, so I measured the distance from the clutch end plate to the groove for the snap ring...same thing.

99 Honda Accord Transmission Recall

1999 Honda Accord Transmission Rebuild

Thanks to Mr. Bill & Manny for the help and lending me some tools I didn't have to make this easier. And thanks to Rick for the cooler that was exactly what I was looking for!
I have since put about 500 miles on the car and it works great. Wow!