I think your "gap between rubber part and metal" is the dust cover. I don't know how critical it is, but it would bother me to know it's in there not seated properly. Ya just gotsatuz seat the lip of the seal into the groove on the slave cylinder.
I agree. I would seat it properly though since it will make it last a lot longer.
A lot of times wheel bearings will only make noise under a certain condition, and it only making noise when you brake, from one side, is probably normal.
Please refer to the manual for adjusting your ebrake. You're correct, no need to jack up the car to do it. It is adjusted from under the cover of what covers the ebrake lever in the car. You don't want to adjust it too tight or loose, so be sure you do it right.
If you did bleed your brakes properly, the pedal height should be about the same as before. Since the brakes are new, it will probably take a little bit of driving to get them to stop well. Try not to overheat them, or use them too much, until you have driven the car through about two tanks of gas. Like many car parts, they need to be broken-in before they will work great.
I know on my VX, I replaced just the rear shoes, and it took at least two tanks of gas for them to seat properly and stop as well as the old and worn-out shoes.
On the never-ending quest for better gas mileage...