Update: 3/8/09
First off, I would like to say I'm amazed that this thread is still on the first page, that is awesome.
In the past year I did an Auto-RX run, added an external filter (Perma-cool) and cooler (B&M). Auto-RX seemed to help slightly, but it wasn't a magic bullet that fixed the problem. I recommend if you have a Honda that is acting up to at least get a external cooler and filter.
From all the reading I have done, I have come up with a theory on why this is happening on these cars. I believe a significant amount of this is due to having garbage o-rings inside this transmission. This issue seems to come up on almost all Civics before the mid-generation facelift(01-03), but also seems to occur on other Hondas as well.
I think this is due to the fact that as rubber ages it becomes more and more brittle. As this happens it is less flexible, which doesn't allow proper amount of fluid to the clutch packs (when cold). This causes the starvation of fluid and the flaring between shifts.
Combine that with required average fluid, no filter (these have strainer systems) and poor cooling and you have the makings of a major problem.
Some notes:
They do not have a traditional filter. They have a strainer that "filters" the fluid out. Basically the flows through a metal screen. You can not get to this strainer with completely dissembling the transmission. You can see some issues that arise when the marginal Z1 stays in the transmission for too long.
These do have a magnetic drain plug that you clean when you drain and fill, but that still isn't as effective as a traditional filter.
The cooler that is built into the radiator does a poor job of cooling. These things eat up Z1 fluid fairly quick.
I believe the torque converter wears faster than average, but that doesn't affect this particular issue very much.
I am going to try some Amsoil fluid next change interval. You can only use Z1 and Amsoil from what I have read. Most others do not work very well in these transmissions. Plus Z1 has a crazy amount of friction modifiers compared to the big 3 fluids.
Right now I have 125K on it and it is still actiing up, but I feel a little better knowing that I have preventative measures in place to buy me some time. I've read on the Civic forums that guys with this setup are still going strong 20k+ after they noticed the issue. Keep up the discussion, I'll try to check back more often and add some input.
Edit: How do I change the title of this topic? I want to include my update is on page 3.