Sounds like you are headed in the right direction. The Precision plasma machine with the C and CNC Bladerunner package are a popular choice for entry level cnc cutting machines. I would definitely recommend using a water table for this machine, it will makecontrolling the fumes and smoke much easier.
Either the Powermax45 or the Powermax65 would work for your application, although I would lean towards the 65 as you have an occasional need to do some 3/8" work....which is near the rated limit on aluminum for the 45. The 65 is also the latest technology in plasma systems, and will provide longer consumable life, as well as having higher duty cycle ratings. Make sure you aske your local dealer for the eductational discount!
Make sure the machine is equipped with a full function torch height control system, critical for best tolerances with any plasma.
Attached is a picture of a recent 3/16" aluminum job that I did with my Powermax45 on a cnc machine. I quoted prices per part, and competed against water jets and laser. I was able to produce parts much faster than the other processes, at a much lower cost, and within tolerance!
Jim Colt Hypertherm