1.) I got the 5945 servo package and have no idea as to what crank arm for the rudder I should use
I always use a 3" arm, we sell the Air Wild arms which are excellent.
2.) Is there any template that exists for cutting out the cowl for cylinder, plug wire, and stock TOC 3MM muffler? Would hate to screw up a beautiful cowl
No. You can mount the engine and get the cowl on without the spark plug installed, this will allow you to find the proper location fror the hole. All it needs is a small slot to clear the plug cap, you don't need a big gaping hole with the TOC-53.
3.) Can you recommend what batteries and how many I should use (TOC 3MM, 5945s, JR 9 channel, 1 rudder servo).
I now use A123 lithiums exclusively. One 2300mah pack is plenty, you can use 2 if you want redundancy. Something like 1200mah nimh for ignition.
4.) How many switches do I need, I bought the MPI that has a battery level indicator along with charging port. Do I need one for the ignition battery as well or can I pigtail them into one switch?
Use 1 switch for each battery. Do not trust the lights on the switch, they are pretty much useless, that's why I don't sell that type of switch.
TF