As an introduction, I have to ask whether, after clutch adjustment using the shop manual and Loud Mouse method, it is incorrect for the alignment of the adjuster notch to be at the 3:00 position and not in line with the notch in the case? Logic tells me that the adjuster's notch cannot ALWAYS align with the case's notch simply because it will be in different positions based upon the condition of the clutch friction plates, right? Correct me if I'm wrong here. I have seen a Honda bulletin in the Bill Silver materials that shows as "incorrect" an adjuster mark that is barely at the 12:30 position. Does the position of the adjuster mark indicate that I have lost friction disk thickness?

IMG_0651 by rzgkane, on Flickr
Next, I am totally confused about friction plates and will ask a series of questions that hopefully someone will take the time to answer for me:
1. How many friction plates do I need? The same number as I took out? I read the excellent write up posted here about friction plates and the like but I still am confused.
2. Can I dictate how many to use since, as the original poster said, Honda used 4, 5 and 6 plate setups?
3. If I currently have 6 and want to use 5, do I need to use a thicker plate?
4. I have a parts motor in the garage and its clutch is a 5 friction disk setup, with each friction disk being real close to 3.85mm in thickness. This is far below the time-to-replace spec I saw in the Bill Silver materials. But could that spec pertain to a 4 disk setup and therefore the plates will each be thicker than the plates in my motor's 5 plate setup?
Lastly, the spec sheet from Bill Silver's materials shows the friction plate standard of 4.8-4.9 and the repairing limit of "4.4 less." What the heck does this mean in plain English? If the plates are below 4.4 they need replacing? Or can they wear down 4.4mm to a thickness of .4 before they need replacing (I would be surprised if this is the case)?
Sorry for all the questions but I am a new but willing owner of a Dream and really want to get this bike running right for at least a moment in time.