soil moisture sensors and watering system using shift registers and analog mux's

You are probably not going to like what I am about to say but there is no getting around it. You need to draw a complete schematic with pen & paper of your entire circuit and take a photo of it with your cell phone and post it. If you have some other means of generating a schematic that would be fine. If the schematic is too large you can use multiple 8.5 x11" printer sheets and show the
lines going off the edge of the page with the note "To page-2) etc.
We can't help you with any code without the schematic. Alternately , you could generate a wiring list that shows which pin on which chip goes to which pin on another chip etc. but that would be a worst case scenario.
No schematic, no code. I don't know if it is possible to describe your circuit with words. (not to be interpreted as "there are no words to describe your circuit...")