Everything except the LDRs are I2C, the Open Log is the I2C version, I believe there is a solder trace you cut to use over serial. The components are tested individually with a Micro, and then added to the MKR1000 one by one. The issue started after adding the HTML, the MKR1000 was not using WiFi at first, it was the last step as I wanted the hardware working before tackling the WiFi side of things. The I2C multiplexer isolates the soil moisture sensors on one channel and everything else on another, the cables to the plants are about 3 meters long, I forget what resistors are on either channel but they communicate fine.
Cattledog, I will look into your comments regarding the serial vs I2C code, I wonder if I copied some code from somewhere else and did not look into it far enough.