Petey's right about the drilling. The drilling needs to be done as the home is assembled.
From there though, we differ just a bit. To run wire along wide joists, I use a router. Cut a 1/2" wide by 1/2 deep slot down the edge of the joists, about an inch from the side closest to the fixture, If you're hanging a fixture under a beam or joist, Use the router first, then drill through the slot and out through the bottom of the beam or joist. So, there has to be a break in the asembly time between first and second floors. you'll need to run all of the ceiling light wires, then as the second floor deck is laid, you need to mark the drilling locations for receptacles, switches etc.. This is also the time to decide how to run your feeders back to the panel. I usually run them low near the floor where the baseboards will cover them. This means that they will be against the outside walls though, which means there will be much more wire used. If the upstairs will be partitioned off with walls, you will be able to use more traditional routing methods. Remember to have them drill the logs from the floor all of the way to the ceiling at your switches.
As fast as most log homes are built, it may be best to plan on being there. It is a learning experience just to see how they go together. Plan EVERY
outlet. Careful planning is crucial here. You may have to remind the builder more than once that he will not be able to get certificate of occupancy if the electrical does not pass inspection. You need his full cooperation.
As for cutting the holes for switch boxes.. I break out the router again. I make a template guide (simply a scrap of plywood with a hole cut in the center to match the size of the box) for each different size of electrical box I will be using. I also make them long enough to sit them on the floor and locate my boxes for me. In other words, If the boxes will work at 16" from the floor to the center, then make the template long enough to sit it on the floor with the hole centered where you want it. This way, all of your outlets will be at exactly the same height. Then for switches, just screw an extension onto your template. Just tack it to the wall with a couple of nails or use screws to hold it still while you use the router. This makes the cleanest holes with the least trouble. You'll need a router with a LONG 1/2" straight cutting bit and a 1/2" guide bushing set. A worthwile investment. You'll find other uses for it after you've used it here.
Wiring a log home is a challenge, but it can be done. You just have to wire it on paper first and plan everything
I also had the pleasure of wiring an old existing log home. It was miserable miserable miserable. You can lose full days on a single circuit if you don't plan them carefully. Conduit or Wiremould along the baseboards looks bad, but may be your only option in certain cases.
Good luck with it.
Post pics if you do the job!
We want to hear about the headaches too