The soldering quality seems pretty good, and I can’t see any obvious problem. One thing to double check if the four pins on the USB connector: those pins are very close to each other and are hence prone to solder bridges.
The resistances you reported are indeed quite low and indicate a problem. The VIN-GND resistance should be about 4.2 to 4.8 kOhm, and VCC-GND resistance should be even higher. So chances are that either there is a solder bridge somewhere, or a component has been damaged after connecting to the sprinkler transformer.
I forgot to ask: does the LCD light up when you power the controller via USB?