Mich,
You do need to do the initialization on the dual plate clutch. It is actually very easy. If your exhaust system is stock it's a piece of cake. If you have headers it is a little harder since you do it from the "front" of the flywheel (engine side).
I recently spend the day with Mark Basch in Phili and got to do this with him first hand. You should do it AFTER the trans has been reinstalled. There are three small threaded holes on the flywheel at about 120 degrees apart (not exactly though). You will need a 5mm bolt as described in the service manaul, or (a trick I learned) is to use one of the small black bolts that hold the plastic covers for the injectors on the engine.
Once the clutch is in and the trans is installed rotate the crank (clockwise) so you can get to one threaded hole. Install the bolt by hand until is makes contact with the guide. You will feel it. Then using a 8mm wrench, continue turning with light pressure until you feel is hit the mid-plate. I turned the wrench with two fingers. Once you feel it get firm, stop, rotate the crank about 120 degrees and do the next one and so on.
What you are doing is positioning the guide against the mid-plate. Once the guide hits the mid-plate you are set. The key here is not to tighten it, like you mean it! Just enough so it stops.
Mark explained this is best done after the trans is in, so nothing will disturb the setting, once the trans is in place.
Also in the service manual there is a whole set of instructions about removing the mid-plate guides, etc. This part is all done already on the new clutch/midplate, (at least on the ACT clutch, but I cannot see it being any different on another OEM style)so for the most part this is a bolt on task.
Another thing we did, which is a really good idea, when installing the pressure plate is to number the bolt holes on the pressure plate(1-9)in a cross pattern, and turn them in 1/4 turn at a time and work your way around the pressure plate accordingly. If not,it can warp.
Make sure you get the clutch disks in the proper positions, we did an ACT clutch and they were marked. Make sure that the pressure plate and mid-plate are aligned with the flywheel properly with the arrows.
One other thing that is very important is the grease type and quantity. You must use the Urea grease from Honda. To grease the clutch splines properly (after the clutch is installed on the flywheel, remove the pilot shaft and apply grease to it, not too much, then insert the pilot shaft into the assembled clutch and move it in and out a few times. That's all the grease you need on the clutch splines. Grease the slot inside the throwout bearing, and LIGHTLY grease the throwout bearing sleeve and clutch fork.
Remember that grease will attract the clutch dust, so more is not better. (clutch shudder)
Let me know if you have any questions.
HTH,
LarryB