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Thanks for the reply. Your comments re a cache of sorts make sense, it's just a bit of a faff (but a faff common to all devices of this kind I guess).
Re the ports, you're right - but having the ports externally would allow you to reduce the size of your housing (as well as reduce the risk of breaking ports in your monolithic device). Of course, it would bring other problems in instead - now you have a different port to keep dry, and non-standard cables. At least you can use a type of port that's designed to be weatherproof.
hamrack
hippy
For mounting on the stem / handlebar etc, something like this;
http://www.ebay.co.uk/itm/360-Mountain-Road-Bike-Bicycle-Water-Bottle-Cage-Holder-Bracket-Handlebar-Mount-/381590459981
and remove the black piece and bolt the D1 straight on? It looks like an M5 fixing.
cache battery -> li-ion only last for ~500 charges which is nothing for touring or long term use and they reduce efficiency to 75% (approx), while super capacitors can't give out the amperage (charge fast, high internal resistance). I've tried both, but it's better to be ultra efficient with what is available.
with the Werk you still need to ensure the USB port runs down at an angle or the pins will corrode. Werk replacement cable cost needs to be factored in, plus availability if you're touring, while a USB extension cable is £0.99 and available mostly everywhere. For this reason I'm reluctant to move the USB port externally.
Regards, Andrew