First off, please, read the tech sheets on the products you are using. The manufacture spent hundreds of thousands, possibly millions of dollars developing the products, they REALLY want them to work well for you. They lay it all out in the tech sheets, from start to finish what you need to do to make that product perform at it's highest level.
Reading tech sheets can be a little confusing if you are not use to them. And they will leave out some little things like your question number 1. Most tech sheets will say something like "Lightly sand dirt nibs and recoat prior to clearing" and that will be it. Some like Sikkens "Autobase" tech sheet has a full explanation of these repairs covering a few pages of the tech sheets!
1. Basically, you treat it like you were "spot repairing" a previous paint job. You lightly sand this area after the base has flashed well and is good and dry to the touch. You have to take great care in not damaging the base with the edge of the paper and use VERY clean water and paper. Most bases are kinda delicate without the clear to protect them. After sanding, you can, if that is the only place you need to paint, just "spot paint" the area blending out onto the surrounding area. Then clear the whole thing after that last application has flashed properly.
READ THE TECH SHEETS! There may be a recoat window you have to adhere to after you spray the base that may be an issue.
2. The vapor will go EVERYWHERE. I mean EVERYWHERE we are talking in your cupboards, everywhere. There are two big issues, real big issues with home spray booths. First off, if the fan doesn't evacuate the overspray it will fall back onto the car and effect the gloss and texture of the clear. If you are going to sand and buff the whole thing, it isn't that big of a deal, but depending how much overspray and how fast the clear flashes that is on the car it can be kind of a mess. Secondly and MUCH more important is your health. If those fumes/vapors don't get out, the concentration of nasties (like Isocyanates) can get VERY high in there make it a VERY dangerous environment.
What protection do you have?
3. You remove the bumpers if you want to do a nice job. What kind of car are we talking about. Most late model cars bumpers come off SOOOOOOO easy I wouldn't even think of leaving them on.
I want to beat a dead horse with this reading the tech sheets thing. It is not only that, the tech sheet has a phone number where you can call, usually toll free, and talk to the tech at the manufacture. It is best to get the right information about any specific issues concerning your paint.
Many of these products from one manufacture to the next are pretty similar technologies. However, there are little details that could make a big difference. For instance, the recoat window with base coats go anywhere from 24 hours to 7 days! Depending on the brand. Recoat on etch primer, anywhere from 24 hours down to 4! Again depending on brand or part number.
If the "R&D" department found that by you wearing a clown suit while painting produced a better job, that would be in the tech sheets. In other words, they REALLY want their product to work, they have it all layed out in the tech sheets.