Well, sounds like you have things pretty well figured out. Just to preface everything I'm about to say, a lot of this is stuff I've picked up, I haven't finished my first build, but I do have some other wood working experience. So, as far as cutting the headstock and gluing an ear on, you should be able to use a hand plane, as long as you can get the neck clamped in a good position. I'm just learnin' to use planes, they are awesome, I really enjoy them and they are quiet, very good in an apartment or condo, like me.
If it's a body blank it should be glued up and surfaced, ready to cut into the shape, so no need for a planer. Your best bet for using the plans you buy are to make a template out of them, or multiple templates, that way you will have them if you ever decide to make another one, plus you can keep the pickup templates you make and use them in every build you have that kind of pickup. A router is your best friend after the templates, bits with bearings are very nice for that. For cutting the shape, you can use a jigsaw if you'd like, just be careful and stay a ways away from the cutting line, then you can attach the template and a router to clean it up. You should be able to do all your contours with rasps if you're careful and take a little time. Practicing before you touch your guitar is always a good idea. An easy way I've seen to get the neck pocket perfect is to clamp the neck to the body exactly where it's going to go, you'll need a center line and whatnot. Then take three perfectly straight boards and clamp them against the sides and end of the neck, after that you can just run a bearing bit along the boards to make a perfectly sized neck pocket, you may have to mess with the corners some to get them to fit the neck, depending if it's rounded on the end or what. For the TOM you can recess it, search the boards, there's a few pictures of them, don't know about a cover though, you can probably do it, but you might have to fabricate your own. Cabinet scrapers would be something I would suggest looking into as well, they are very handy. That's all I can think of. Good luck on your project and post lots of pictures.