Thank you Tony and Trevor for your replies.
I approached Adam @ Pitbull with a few questions, and even asked about placing the body and neck so we could start again (that would cost $190 which is reasonable)
We have decided to try and salvage what is there, which may or may not work out, but it will be a great way to learn!
I like Trevor's suggestion to dowel and re-drill the post holes, and I think this could be a relatively easy way to go about it (compared with trying to remove the neck). I will fill, measure, drill, and use the hardware that I already have. That will leave a couple of dowel plugs visible, but I thought the easiest way to cover these and the gap at the neck is to cut a new pickguard that will cover any patches.