Yes, I do all my own maintenance... have been for almost 30 years of riding HDs. I wouldn't trust anyone else with my machines.
What I did to run the wires was to securely tape a piece of 16 gauge wire to one end, then pulled it through with the old wire. Then I attached the new wires to the 16 ga piece and pulled it through. It's just like using a fish tape to pull wires through a wall in a house. Of course, you can route them anywhere you like. It's your bike. Do whatever you feel comfortable with.