I can explain how you can have the best of both worlds in one sentence: rout the neck pocket first, then use your body template on THE BACK OF THE GUITAR. Just flip her over. If you mark your centre lines and such, then they will align perfectly on the back.
I also agree with getting all your parts (or as many as you can) before doing any serious work. I know it's hard with all of those lumps of wood staring at you wanting to be worked, but the fact is you can't play it until the parts arrive, so in the meantime, just chill.
Do you have access to a bench drill. If so, I can teach you a number of tricks.
Joining the body timbers: a hint.
Instead of sash clamps, buy yourself two slabs of 1/2" timber which are as long, and slightly wider than the thickness of the body wood. Buy 4 or more lengths of threaded rod, some nuts and some wingnuts. Drill holes in the timber put the rods though and you have yourself a homemade clamp, adjustable with the wingnuts. If this is unclear, I can show you with pictures.
Good luck!!!