Ryan, did you get one of these? >> http://fm-xweb.frymaster.com/service/udocs/Manuals/819-6506%20FEB%2010.pdf
Just wondering, because I didn’t. A frymaster rep rolled through town some years ago and gave up what seemed an impromptu class on LOV fryers and SMT connectors, called me certified and went on his way. With that, I DIDN’T get any sort of manual.
In my three subsequent years, I worked on exactly one LOV fryer and cursed the new SMT connectors on CM3.5 and M2000 controllers. I personally don’t ever expect seeing another LOV fryer since I left the field in 2012.
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Not much help here, but I’d question any of the SMT connectors first by wiggling-n-jiggling them around for maybe correcting any faulty connections. THEN…maybe a bad connection in the control wiring which runs that pump. Your problem seems to center around the ATO board output, which you’ve already checked power to.
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Sorry, but that’s all I’ve got for you. I really have no idea, so just throwing some possibilities out there. I’m sure you’ll get it though.