I'll take a stab at some of the questions...
1) IIRC, known bug
2) AFAIK no one offers finished docking stations. Main trouble for anyone to produce them is lack of sleds. Do a search for the thread on spare docking connector (the connector that sits inside the docking sled - this is tha main hurdle) group buy.
4) AFAIK, no one has made a larger one. I've made one in aluminum, but that was about same shape/size as the original. Shouldn't be a problem to do a 'mushroom' shaped version where the 'head' is wider - and how to secure it. As long as the 'head' is slimmer than the hole in the fascia you can use a hidden grub screw... Is your unit a MkII or MkIIa (round or D-shaped knob shaft? With the round shaft you could probably do without grub screw and use O-ring instead. If one has access to a CNC mill and small bits, one could probably do a D-shaped hole to start with... Another problem is that you might block the IR receiver that sits next to the knob. Might possibly be solved by drilling holes along the circumference, both for allowing IR to pass and for grip.
5) Do a search for jEmplode and mp3tofid for two projects that might interest you. There's also the linux command line tool, emptool.
6) IIRC, there's checks on more than the filename only when deciding a file is a duplicate...
7) see 5
/Michael
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/Michael