1. Do I remove my A1200 from its shielding and bolt it directly to the EZ-Z4 backplane with 2 screws and the port nuts on the back? Do I need an insulation layer, etc...?
Yes, you have to remove the shielding, there should be some "riser" screws that come with it to hold the MOBO away from the case, then you screw the mobo to those. (Same principle as mounting an X86 mobo) I'm not sure how to remove the shielding without damaging it, I unfortunately destroyed mine in the process. (The shielding, not the mobo) Perhaps one of those keyrah thingies would work, if you want to use the 1200's empty "shell" + keyboard as a ps/2 keyboard? (something I've been toying with myself, but not looked into a whole lot)
2. My PC-Key has a chip on one side. Do I install this into the A1200 keyboard socket, sans clip, with the chip side facing me as I look at the A1200 from the back? (Port side). Does the socket side of the PC-Key bolt on the back of the EZ-Z4 at the bottom hole to the right of the power supply?
I believe the chip goes towards the back. Been awhile since I've done this, though. Google Images did reveal this image, though.
http://eab.abime.net/picture.php?albumid=95&pictureid=518 . (its kinda fuzzy)
3. There are 3 connectors, a 22pin connector near the ROMs (clockports?), 34 pin connector CN11 (Floppy?), and 44 pin connector CN16 (IDE?)
The 44 pin (should be about 3" from the PCMCIA port, on the left) is IDE. The floppy port I believe is near the 4-pin HD/FD/Power LED header. The clockport I believe is down and to the left of the floppy port. (wishing I was posting this 4 months ago, when I did essentially the same thing)
4. The EZ-Z4 Tower has a floppy facia. Is this for an Amiga1200 internal floppy? Is this the same that is currently available from amigakit?
The "fake" button on the A1200's will get in the way, I think removing it should work, and the blue button should reach the "real" eject button. Not sure, as I put a HD floppy in mine. Otherwise the floppy port below it should work. (Works with an IDE zip drive too, if you have one)
5. At a later time if I decide to get the 6 port expansion board and an accelerator, will it be easy to install or will I need to remove the mobo and re-install?
The PSU might get in the way, if you use a PC one. That's held in by 4 screws, and probably the easieast thing to remove, assuming the cables are long enough to lay it somewhere convenient without having to disconnect them.
I have some pictures of my setup on webshots, I snapped a few while towering my system. They might be useful.
http://entertainment.webshots.com/album/570455108dloPxV(Ignore the use of zip-ties as a HDD mounting bracket...) :-D