OK, measure the voltage from the top of R11 to the back metal face of U1 (that's a nice accessible ground). By the top of R11, I mean the side of R11 that's the furthest away from the 10 resistors GR1, ..., GR10. That's the PWM output. Measure the voltage of that at zero throttle and at full throttle. It should go from 0v up to 5v. If that's OK, the next measure the voltage from the left side of R15 to the back metal face thing of U1 at zero and full throttle. If that goes from 0v to 5v, then measure the voltage from the bottom of R16 to PH1 or PH2 (or B- bus bar).
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