Well personally I recommended mini-itx not atx, unless that was a typo. High end mini itx/atx boards accept the same processors and graphic cards as huge boards. I think most people are recommending them because they are smaller, lighter, and will give you more options for mounting your other components in the box.
Sorry I kind of ranted before, I'll try to see if I can actually give some input on the questions you asked.
1. As for static electricity I'm not entirely sure on this one. It could be as simple is drilling a small hole and putting a bolt through it with a wire that you touch to the ground of of your power cable before your plug it in to discharge it. I know they make spray films that supposedly guard against static and big air ionizers that remove the charge.
2. I use a corsair H60 and the thing is pretty solid with a nice low profile and cools quite well. I don't see with it as long as you don't pinch the lines or try to force them into a position they don't want to go to. I think if your case has a big enough shock to mess with the cooler most of your other components and monitor are probably broken.
3. As for the hinges you could throw one of these on each side http://www.amazon.com/Rockler-Large-Lid-Support/dp/B001DT3KEU/ref=pd_sim_sbs_hi_5
. Would beef up the support greatly, but remember you are attaching them in plastic, you would need to bolt them, not screw them in and your mileage will vary compared to attaching these to a piece of wood. I've noticed that thing monitors seem to get a lot hotter (to the touch) than thicker monitors since they separate your touch from the hot components. You could use adhesive heat shielding material, the kind of stuff they use to protect car bodies from engine heat, but you are still going to have to vent that heat out in some way. I wouldn't put a piece of plexi glass in-front of your monitor, it smudges and scratches and may even cause some kind of refraction at different angles.
4. For your ventilation your two hottest components will be cpu and gpu. It kind of depends on what cooler your use, if you go with the corsair hydro you can mount the radiator away from the other components. For your gpu I would recommend one with a blower (not open face) so that it shoots the head straight out of the case. I don't think fan grommets are necessary, they do reduce vibration and look cool though.
5. I have never used one of these, but I think it could be awesome for your build
It would allow you the freedom to change the orientation and placement of your gpu. Not having your card sticking up perpendicular to your mobo would free up a ton of space, and you could mount it more securely with some kind of bracket to avoid stress on your pci-e slot.
6. I mean it shouldn't be a big deal what sized hdd you use or using an ssd if you mount it in a way the it is secure and not getting jolted when you set the case down. This isn't a traditional laptop where you will be walking around using it or dropping it off a table while the hdd is spinning. Some laptops have drives that can sense a fall and freeze the disc to prevent damage, but in your case if this thing drops from a significant height while its open and being used that's the last thing you would be worried about breaking. SSD's do run a tad bit cooler and of course they waste HDDs in read/write and boot times, I personally won't be buying/building a desktop or a laptop for myself or anyone I do a build for without a system SSD.
7-8. One way is to cut a piece of acrylic the size of your fan/vent holes with mounting tabs that bolt onto your case with some type of gasket material between the case and the acrylic to make a seal, it would be kind of time consuming to take them on and off, but they would be used in transport/storage so it wouldn't be the hugest deal. Another way would be to cast silicone "caps" that press into the holes by pressure (and key notches cut out to help them seat properly and lock in). It would be kind of cool, but not that easily to do and the mix is quite expensive. Ugly options would be trash bagging it or duct tapping across the holes well.
9. I mean I'm sure its possible for you to go smaller, but it just adds to how hard it is and time consuming it will be, its already going to be enough of a challenge.
10. I wouldn't even go there, if the point of this is to have a desktop experience then putting in and old laptop screen with a crappy resolution and color wouldn't be counter productive, plus it would be a pain getting it to connect to the pc itself as well as to power, also a lot of the screens use the chassis of the laptop to aid in the cooling so if you are just resting it against insulated plastic that isn't going to help.
As for your pics that cpu cooler looks so massive, I'd definitely recommend going with the corsair hydro over that, those big coolers work well because of the huge surface area for airflow, and in this case, no pun intended, the airflow is going to be tough anyway. Do you plan on sli or x-fire or something? A single gpu should be more than enough if its a good one so you really don't next the extra pci-e slots.
Not sure if you have looked at this route, but depending on your games and your monitor's resolution it *might* be possible to use amd's A10 apu. If you are gaming at 720p, which with that size of a monitor is a real likelihood, the A10 can pull decent frame rates in a lot of games depending on the settings. If you go this route then boom there goes your discrete graphics. You could use a FM2 mini itx board. You could throw in 16GB of ram (High speed for apu performance), a pico psu that is like a laptop power cord, and a ssd. In theory it would be a sick little computer that games and Photoshops great all while being smaller than a textbook.
^^^ I've looked into doing this build like 4 times and have almost pulled the trigger, but haven't managed to do it yet.
These are the kind of dimensions we are talking about with this build 8.7" x 3.1" x 8.4". That includes all your components minus the external power adapter and your monitor of course.