lol, people have some big ambitions. I'll answer some of your questions, mainly the ones I know the answers to. Unfortunately there are some things I don't know and I'm not one to make things up for the sake of spouting off on forums.
The materials are substantially more durable than the plastic casing of the zaurus. The casing Is relatively thin and of marginal quality. Not only does a composite/resin construction have higher tensile strength than plastic (by several orders of magnitude), but the epoxy coat is quite scratch resistant. What's more is, a coat or two of automotive clear-coat will allow you to simply rub off every day scratches with a light compound. Not to mention it looks great. (I WILL have some proto pics up when I have time to finish it off. I have the mold and the materials, all thats left is pressing it in and setting the epoxy. As I said I am a full time employee and a full time student, so time is at a premium)
As for the many different designs you mention, this is quite another story. I am producing the exact replica cases because I have a C-1000 on-hand that I casted molds for myself. Thus, I know exactly what it is, and how it should turn out. When you get into custom work, you are adding many many variables that often are lost in explanation. Without a very good set of diagrams or a CAM model it is very difficult for me to know just what you want. The most feesable mod at this point is a larger battery bay (perhaps by simply adding an extra milimeter or two to the entire bulk of the case) and external access to the internal CF drive. However, at this point I have not yet got a C-3k, so that will be on hold until I decide I need one.
If you have complex ideas on hand, you may consider creating your own! I have been doing composite for a while now, but there honestly isnt much to it. I do it as a hobby, in support of my other hobby, which is motorsport. If you do it yourself (or at least design your own mold), you can simply cast the case of your own Zaurus, then hand-carve any additional amenities or case modifications. This way you have exactly what you want. However, precision work with composites is difficult, and openings are generally cut after the epoxy has cured, making it a chore to finish the cut surfaces. The stock form of the clamshell is relatively simple, making it an ideal choice.
As for a case, I am prototyping a holster-style, formfitting case for the Z. It will not include a capacity to access the CF or any other external jack due to its compact nature. I am making it primarily for me, and in a limited production as with the case replacements. The case will probably have small holsters to hold your CF cards externally, and the case itself will be waterproof as I mentioned.
Once I have all my molds perfected and my technique refined I'll probably reach a capacity of about 10 units a month. This will depend on my availability. Also the availability of carbon has become a major concern. Aeronautical companies seem to be sucking up composites faster than factories can produce them. But, in either event, I forge ahead! Luckily, the limited supply of carbon I have been able to secure has been residual stock at a very reasonable price. The $100 price point was actually a bit high, and I'm hoping to produce for less. Again, there is little to no profit to me, and I will include a material invoice for all parts used in construction to ensure this. The only money I am making will go to pay for my paypal fees, taxes, post, etc.
If you have custom designs and can provide engineer-grade diagrams or CAD models, I can produce your custom design for a very modest premium. I will prioritize custom projects ahead of the normal cases. However, if you are in an excessive rush, or require very extravagant modifications, I would highly suggest investigating a CNC machined option in a material like aluminium, which lends itself well to such design. Composites are finnicky to work with when it comes to precision manufacture. This is a hobby, which for me is placed on one of the back burners. Although now I have a good idea of the level of interest to expect when I begin serial production.
Thanks for your replies so far and I will be more than happy to field any other questions you may think of. I'll have some pics of the raw materials and my ceramic molds shortly.
EDIT: Ah yes, as for screen protection:
You are correct in assuming that a britle screen protector should interfere with the touch sensitive membrane. In addition, I haven't had experience integrating a material such as glass or lexan into composites before. A resin shell is possible, but removing the touchscreen functionality from the Zaurus seems nonsensical. Also, the unit would not be able to close properly, and it would likely interfere with the exotic rolling hinge design of the clamshell. It is possible to completely redesign the case to close flush an include a hard screen protector, but then you must consider, what is to keep that surface too from being scratched!
I think what is best is simply to replace the outer shell as I planned, which will provide added protection from every day abuse such as drops (I also failed to mention that the epoxy coat provides a limited degree of shock resistance), scratches, spills, babies, medievil crossbowmen, spears, mongolian hordes, and zombie pedestrians, while making a clean, good looking Zaurus.
If you are obsessed with a modified, ultra tough zaururs, there are plenty of precision machine shops online who can laser cut your CAD model for very, very reasonable prices. The primary appeal of this case should be its good looks with the fortunate side effect of being tough!