hi and welcome to the guild
1. no ... what I would do would be to take a copy of the layer without the bevel and put on top of the other - then cutout the middle so it only covers the problem.
2. not quite sure what you mean - but you can put a mask on a group if that helps. I often CMD (CTRL) click on a layer or mask to get a selection choosen, then go to the relevant layer and activates mask there, that is pretty fast.
3. what isn't matching - the dark between tiles? You might consider making the tiles bigger and then drawing an extra shadow manually
4. none - you can't go to 300 dpi from 72 without having to tune and/or redo stuff. Photoshop can do a lot of stuff but everything can't be automated.
Looks like you got a good start on mapping - looking forward to seeing more ... you might want to make a WIP thread on your map while you work - then you can get help and critique