Yes, that's right. PCIe is fully backwards and forwards compatible, so far - you can stick a PCIe 3.0 card in a 1.0 slot, and vice versa. And yeah, it's easy to get a card that's too bulky, particularly with that price range. What I would do is take the card dimensions and make a rough cardboard mockup before buying. For $200 it's worth feeling a little silly, no? Try to get it in there without it bending or coming close to any non-flexible components. Take note of any capacitors conveniently placed in the way of your card - on your current board it looks like you might have at least two that might cause problems with enclosed fans, and the southbridge heatsink (the white ribbed thing in
this picture) also appears uncomfortably close. Otherwise you should be ok - you have a microATX board in a mid-size ATX case.
Graphics settings - it depends greatly on the game. As I said, some games are optimized for this more than others, some games don't even slow down as they're loading textures in favor of noticeable 'pop-in' (which is what I prefer, or even wireframe, so we're in the same boat), and some don't have textures (and shadow maps, etc., basically anything that needs to be thrown to the card for calculations) lower than what PCIe 2 can stream comfortably. The shittiest console ports don't even have graphics settings you can change much at all.
If you're experiencing repetitive 'jerky' lag, particularly while moving, there's probably a bottleneck here, with your card's memory speed and size, or you're running it off of an external hard drive or something. That or your CPU and RAM is inadequate for whatever else they're doing as you move, but this is surprisingly often less of a problem in more mainstream games.
For your motherboard, the only reason it's likely to be damaged is static and/or short circuiting. Make sure to insulate it from the case using those plastic/rubber dealies, touch the side of the case often as you're working with it (or if you're really paranoid/live in a dry area, a grounding strap couldn't hurt), and don't work with it on carpet. Take it outside if you have to, the light might even be better. Above all, use patience more than your screwdriver - move everything slowly so as not to jar any caps or the underside of the board. Don't try to force anything that seems stubborn without looking for why it might be giving you issues. Loose screws can be killers - try not to get too frustrated when you inevitably drop one and it somehow gets
underneath the board you just half-installed. This -will- take you longer than you expect, and if you go into it knowing that, you should be fine.