That doesn't look too bad at all, top effort...!
I can obviously see the low spots you mention, but can you actually feel that they are low, by hand? If it is negligable, ie, you can only just / hardly feel them, then high build primer should do the job... If they can be obviously felt, then maybe a small skim of filler...
When sanding the filler, try to use long 'swishing' movements, really using your arms and body to get long movements, rather than working on one area, then the next area....(if that makes any sense....i know what i mean....!)
Also, try to 'cross hatch' the sanding....attack from one angle for a bit, then from another angle, etc...that way you shouldn't get any flat spots and the curves should flow...
RE the bits that have repelled the water....that wouldn't be where your other hand tended to rest when sanding..? Natural grease from hands could be enough to do that.. a good spirit wipe should sort it, but if not, a more aggressive rub down might...., but if not, rip the top off with 80 grit untill its gone, and a skim of filler there too.. If the problem persists, definately point it out to the bodyshop, they should have no probs with it...
Hope my ramblings might help a bit, look foreward to seeing it in paint...I'll shut up now....
