I have some major questions about bombardment.

One: How does bombardment work with blocking and hindering terrain? Is there still a -2 penalty to hindering terrain like there is with blocking?

Two: After an attack is resolved (drift calculated damage given etc)
a) does the token stay there, and next command phase the bombarder can attempt an attack again?

b)or is the token removed, and when the bombarder wants to bombard again he repeats the process?

1. You only get the -2 for blocked lines of fire, if the token is outside the bomber's front arc, or if the bomber is based by opposing figures. I'm not sure, though, if the +1 defense modifier for firing into (or through) hindering terrain applies.

2. Option B is the correct choice.

But does the bomber get a -3 to his attack for shooting through hindering terrrain (-2 for being obstructe and another -1 because of hindering terrain rules). Does he incur any penalties for shooting OVER (which is what it is) hindering terrain?

Hindering terrain does not affect your attack score. It affects your target's defense. Same basic effect, but an important difference with the Rule of 3. So, no, there will be no -3 to hit, just a -2 and a possible +1 to the targets defense.