Rebuild Project: PM161612 aka Novice Needs Help

A Prusa-Mendel with a build envelope of XYZ 16"x16"x12" was given to me. I know nothing about these things but I've decided to rebuild it for the experience before going to the expense of building a new one. It's easier to swallow the cost if I blow it up. Please help if you can.

Progress so far:

1. Cleaned the machine and lubricated the all-thread lead screws and guide rods.
2. Identified the controller as an Arduino Mega 2560 controller.
3. Installed the Arduino Software and configured it for COM6. Windows successful recognized the driver.
4. Installed Repetier Host 3D Printer Software
5. Established communication and moved X, Y, and Z axis using Repetier in manual mode.
6. The motors are Minebea-Matsushita stepper motors: X and Y axis use Part Number 4K1-1106 Type 17PM-K901-G2VS; Z axis uses 2 motors, Part Number FH5-1034 Type 17PM-J801-P1VS.
7. Dual extruders have the same motors as the Z axis.
8. I think the hot ends are J-Heads.

Issues to address:

1. Firmware: I have no idea what firmware was installed on the Arduino. I think I will overwrite it with the Repetier Firmware so that all Repetier Host features are supported. Is there anything other than Repetier that I should be aware of and/or use instead? What information do I need to set up the firmware properly?

2. The Z axis all-thread lead screws are jamming in both directions. I'm not sure if the problem is in the threaded rod/nuts, motor, alignment, drivers, or all the above. There are 2 motors so they could be out of sync or turning at different rates but I don't know how to check this. There is a support bracket missing on the left Z axis guide rod which is probably contributing to it.

3. Calibration: X, Y, and Z axis are not homing properly and are pretty far from where I think 0,0,0 should be. I'm not sure how to calibrate this and need some help figuring it out.

4. Build plate is belt driven and wobbly. When it stops it wobbles. I'm not sure if it's the belt or mounting hardware. I can tell that the bearings are probably part of the issue. They do not all touch the guide rods.