1. Does the kit come with ferrules for the back of the Tele? if not how do I secure the strings?
Some T style kits come pre drilled for string through and should include ferrules - can't remember for ATL kits if they are - otherwise they will be strung through the bridge. If it is pre drilled for string through and you've not got ferrules - reach out to the team and they'll sort it out pretty quickly.

2. My neck plate doesn't align very well, in fact, it hangs off the edge of one side a bit.. it that fixable? (the photo makes it look a little worse than it actually is.
Might leave this for some others - haven't seen this before.

3. The amount of wood is very thin at the top part of the neck pocket, is that normal?
Do you mean the curved bit in the first photo? If so - yes it does get thin - its a result of the routing of the neck channel and the edge of the guitar. Treat it carefully and once the neck is in place and you've done a finish, it will be fine (has been for all of mine so far).

4. Might as well ask for strings - who do I contact directly?
Best to contact is Service at pitbullguitars dot com.