I did the same when I put in my floor. I used the filler neck, held up to the hole, rotated around a little to see the correct angle, then started gringing the hole out with a die grinder. I also installed the tank from below to eyeball the angle. I kept enlarging the hole till the filler tube lined right up. Funny thing is, the old hole was HUGE and when you get a new rubber boot, you'll see how big that hole can be and still be covered. I can send up a pic of the smaller hole after I get home if you still aren't sure.
Rob