I haven't planned out my guitar very well either, but I find it gives me the oppertunity to learn how to fix mistakes and turn them into design features.
I don't know what shape you are planning to make it, but if the wood is too big couldn't you just cut it smaller, or change the neck join?
As for the neck not being as thick as the body for a neck through, I think you could probably rout out a channel in a one piece body blank and fit the neck in that way.