This is the original poster of the run cap advice (Not a heater repair guy), I had to change ID because my account was locked out.
The run capacitor replacement has made my Pentair minimax run without issue since my first post (Dec 2011). No more E04s, E05s, doesn't work after a rain, works sometimes, starts sometimes or other flakey electrical behavior issues since the original post. The fan "ran" for a long time with the bad cap, but was blasting so much noise all over the place that the controller threw those error codes around till I fixed it. About a month after replacing, the step down transformer to the control panel blew, maybe because of the cap also, so I replaced that also. (that one was easy, no LEDs lit, and everything was working fine for a month or so before it gave out, so I know the cap fixed the cause of the E codes)
If you need to replace the cap, just turn off power, remove the silver air vent housing and screws, lift the top plastic cover remove the existing cap, and take the part with you to match. It should be marked with a capacitance and voltage, and is called a "run" capacitor.
It is $10 or less, and literally takes 15 minutes more than the time needed to get the part in hand.
I got mine on line, but I also saw people go to Home Depot, HVAC (Heating Ventilation Air Conditioning) places, etc.
I wouldn't do this first for obvious mechanical, gas, or flow issues (ie banging noises, no gas, etc) but would try it FIRST for overall flaky electrical behavior.
One thing I just noticed is that you replaced the motor, which should have come with a new cap. This may not be the issue with your spa, unless the motor was a used one.