HI Keegan,
The last post was last year, I thought I would respond on your post.
My husband & I also own a John Deere 4310 tractor (NOT EHYDRO).
Our tractor was flooded when we bought it. My husband is new to tractors & has been researching.
We finally got the tractor running after about a year. when we first bought the tractor it ran, got it home it stopped running.
Anyways.... regarding the wire you are talking about. This is the RED-C (near clutch pedal)
it's function is for the cruise control option, it is also for the diverter valve wiring harness.
I am not really sure regarding the PTO on your tractor. On our tractor it looks like someone cut those wires.
Bonnie