Driving a charge pump with a Mesa 5i25 stepgen

No, that should be in hardware

You can verify by looking at your current pinout with:

sudo mesaflash --device 5i25 --readhmid

IO Connections for P3

Pin#  I/O   Pri. func    Sec. func       Chan      Pin func        Pin Dir

 1      0   IOPort       None           
14      1   IOPort       PWM              0        PWM             (Out)
 2      2   IOPort       StepGen          0        Step/Table1     (Out)
15      3   IOPort       None           
 3      4   IOPort       StepGen          0        Dir/Table2      (Out)
16      5   IOPort       StepGen          4        Step/Table1     (Out)
 4      6   IOPort       StepGen          1        Step/Table1     (Out)
17      7   IOPort       None           
 5      8   IOPort       StepGen          1        Dir/Table2      (Out)
 6      9   IOPort       StepGen          2        Step/Table1     (Out)
 7     10   IOPort       StepGen          2        Dir/Table2      (Out)
 8     11   IOPort       StepGen          3        Step/Table1     (Out)
 9     12   IOPort       StepGen          3        Dir/Table2      (Out)
10     13   IOPort       QCount           0        Quad-A          (In)
11     14   IOPort       QCount           0        Quad-B          (In)
12     15   IOPort       QCount           0        Quad-IDX        (In)
13     16   IOPort       None          

Looks like it's there.  What else could be preventing the waveform from getting output or the G540 from being able to recognize it?

It may be that the chargepump output doesn't have enough
high level drive for the G540. You might try jumpering the 5I25
for 3.3V compatibility on P3, This will provide a bit more high side drive.

W3 jumper is in the UP position (5V tolerance mode enabled).  I had it that way when things were working under 2.5.3.  But I can give it a whirl tomorrow and see if it does anything.

No luck with the W3 jumper in the down position.

What to look at next?  Can I see what's going on with pin 16 output using HAL scope?  How is that done?  I've never used HAL scope before.

I would set the frequency very low (say .25 Hz) and measure the
high and low output voltages on pin 16 with a voltmeter