rear: visit the CycleX website, they have 11" shocks;
front: yes the CB650C has 2" longer forks, I have a spare set of these layin' around
drill holes: not very recommedable as said.
forward controls: make it as you like it, just make sure the brake proper done.
and for the fender, check egay regular or the highest recommendation is to look around at a salvage yard, motor barn or any place where are lots of old bikes.
one day you'll buy something that doesn't fit at all and the other day you find the perfect one, the first will be a spare for the next bike you build
and since you're new, welcome, you 're here to learn.