#1
will changing from 9s to 11s w/ a wound G (11 to 52) mess up my guitar's neck?

wat will extra heavy strings do to the neck and tone? (13 to 56)
#2
it will put a bunch of extra stress on hte bridge, when i did it on my strat, i had to go in and get it adujusted. i would do it just to be safe.
"Blues is what you got when everything else is
gone." - J.Lansdowne
#3
You'll immediately notice the action higher from changing the gauge. You should adjust the truss rod whenever you switch gauges.

Extra heavy strings will have a fatter tone, and again, you'll have to adjust the truss rod.
Gear:
Gibson X-Plorer Studio Yellow
Orange Tiny Terror
Orange PPC-112 Cab (2 stacked - 1 open backed)
MXR Phase 90
Fulltone OCD