I did a lot of work on small things this weekend. I finally greased the rails, adjusted the endstop tabs so they meet the endstops correctly, reloaded the firmware, and rewired the 12v system (it was very sloppy and would have caused problems eventually).
I now have all 3 axis moving smoothly. My only problem is that the X and Y axis move in reverse. They worked fine when I was jogging them but as soon as I tried to home them they shot to the wrong end of the rails. I don't have my control box wired up yet so I had no emergency stop button but I had my hand on the plug for the power brick so I was able to pull it and shut things down without any damage. I tried to reverse the direction of those two axis in the firmware but it had no effect. I suppose I have to dig deeper into the code. Either that or change the wiring of the motors themselves. Strangely, the Z axis moves correctly and I can home it without any problems.
I also worked quite a bit on my extruder. The hot end is assembled as well as most of the rest of the parts. I just need to epoxy the peek insulator into the main body of the extruder. My main problem now is that I still can't get the gears off of my used stepper motor. I am going to order a new one today and I will just have to wait for it to arrive.
I will start to assemble my control box this week. It will clean up my workbench a bit and I won't have to pull the plug anymore to shut the steppers off. It will only contain the power brick, a lighted on/off switch, for the 12v system, the emergency cuttoff, and the PID for my heated bed but keeping those things neat will be worth the effort.