I think this discussion came up on the forum a few years ago. Having some gap there is pretty normal. Fight to bring it together as best you can and then move on.
I reckon when I stopped fighting and started gluing, the gap was maybe on the order of a 1/4" in some places.
As far as making sure everything is in alignment, there are two things I did to make sure the hull was level and there was no twist: 1) Measure back from the bow to each corner of the transom, 2) make sure the boat was level athwartships with either a straightedge and bubble level, or using the old water-in-a-clear-tube trick (I used both, actually). To make adjustments, I found that putting shims under the cradle was sufficient to get evertyhing perfect.