Yes, this can be renewed over time with sanding etc. I am unsure of how much of the stain you can remove by sanding (it will definitely soak into the wood and remain visible longer than polyurethane). I've removed loads of lacquer and polyurethane for refinishing wood, but have yet to try removing stain.
Yes, you can fill old screw holes by drilling them out and gluing a dowel rod into the hole (use a good wood glue for this, my preference is Tightbond). This is probably as good of a fill as you can get. Sand the dowel down until even with the desk.
Regarding tools, that really depends on what how you want to build this and how good you want it to look. Are you using rough-cut wood, or something that is already pre-sanded and ready to go (something you buy at the big-box stores)? If you start from rough-cut then you really need a joiner, planer, good table saw, possibly a router, and ideally a drum sander. That's unrealistic for a single project.
On the other hand, if you're going to buy a solid piece of oak that is already cut and joined (e.g. something that is already 4' x 6') and you don't really care how it looks then you just need something to cut it (a circular saw or even a hand saw).
The point I'm getting to with the tools is that we need more information regarding how you plan to build this before we can help you build it (this probably fits better under woodworking than home improvement anyway). How you plan to build this will dictate what tools you need to do the job. Best of luck, this might be a fun project!