Did you get a really good look at the MFS connector when you replaced it? Sometimes the contacts can push out the back of it, common fix is secure them in place from the back with hot glue or epoxy. I mean the mating wiring harness connector, not the MFS itself.
I'd also wonder about the wiper motor, would run a fused jumper wire from battery + to wiper contact #4 (low speed, white wire) then try #5 (high, dark blue/orange wire). You do not need your MFS set to have the wipers on for this, they would run continuously in low and high mode.
If wipers run fine in both those speed with the jumper wire, next thing to try is shorting the wiper run relay, pin 2, yellow/white wire to ground. If more convenient you can unplug the connector from the GEM where it's connector position 19 (still yellow/white wire), then with that shorted to ground, and ignition switch in run or accessory, the wiper run relay should trigger and the motor will run at low speed. If it does not, I'd suspect your GEM and get a pull from a junkyard, or open it and look for failures, or possibly before going to this much trouble, use a multimeter and measure for resistance on the following wires (see attachment below), all should be under ~5 ohms or so. If not, it's a sign of a wiring or connector fault.
1) Wiper Run Relay #2 (yellow/white) to GEM #19 (yellow/white)
2) GEM #21 (gray/red) to MFS (gray/red)
3) GEM #22 (pink/yellow) to MFS (pink/yellow)
Also pay extra attention to the MFS mating connector pins for #2 & #3 listed above, if they got pushed backwards in the connector as mentioned in my first sentence in this post.
Also there are those two large wiring harness connectors in the engine bay, that you might unplug, inspect, and replug.
Sometimes a gremlin can be caused by the smallest thing. There are 2 large wire bundle connectors on the firewall. Both are held tight with a 10mm bolt. Any bad connection in either plug can cause just about any issue. from bad transmission shifting, bad o2 sensor readings, no start, no...
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Something else you can do is use a multimeter to measure for 12V on the motor #4 or #5 wire harness connector pin to see if it's getting steady power when acting erratic/intermittent. When it acts intermittent, does it seem like it is waiting the same precise amount of time to sweep the blades again, or does it vary? Does this change when the vehicle is parked, opposed to being subject to road vibrations while driving?
Wiring diagram attached.