Ross, next time use a hole cutter. Scribe out the line (don't cut all the way through). Use a reamer to open up a hole in the middle and make pie cuts up to the line. Bend it in and it'll break right at the line. For the side windows, scribe a line with a hobby knife and do the same thing with the reamer as you did to the cooling holes. It can also be done to the wheel openings. Nice clean lines and no jagged edge. Just clean it up with 220 grit paper. For the wheel openings, wrap the sand paper around a soda can and just start twisting it in the opening. It'll smooth it down.
For an almost perfect 2" opening in the front (if you don't have a hole cutter), get a spool of teflon tape and trace the outter diameter with a sharpie. Scribe along the insde of the line with the hobby knife and use the reamer and pie cuts as I said earlier in this post. That will give you a hole that is 1.97 inches. For the rear, cut out the whole window. It's ROAR legal todo that. What I would do is make 2 two inch holes and cut a straight line from the top of one hole to the other. That way, you'll still have enough meat in the rear for support.
Another trick is to get a very long zip tie and loop it into the tank lid and extend the end out the window. If your chassis has a slot incorporated into it (like the serpent) then clip the lock off another zip tie and lock it into place. That way, when you have to refuel the car in the pits, your pit guy can just stick his fingers under the zip tie lift the car and open the tank all in one shot.
Remeber, we're not supposed to refuel in the pits. Car is supposed to be lifted off the track and refueled. Well, that's what is supposed to be done. At a ROAR sanctioned event, if they catch you that's a stop and go penalty the next time around. Besides, it makes good practice.