So it took a little longer to get around to tinkering with this than I had hoped but things have come along well.
@dmills
The ground is a hexagonal plane on the bottom layer. It's a dev board, a chinese knock off unfortunately. Decoupling isn't great as there is potential for noise to feed through both the signal and power lines. I had considered adding an opto isolater for the sake of the signal line but question its practical value if noise can still couple through the power line. I wasn't aware that a resistor alone could aid noise suppression. How does that work? Parasitic inductance?
I think what you mentioned about the overly high input signal may of really been the cause of my issues here. The actual voltage being fed into the FPGA was around 4.5V. The FPGA is an Altera Cyclone IV which has internal clamping diodes to protect from over voltage. I thought I may be able to get away with it, thinking the clamping diodes would bring the signal down to 3.3V. In reality I think the diodes weren't stabilizing as "cleanly" as I'd hoped hence they were sinking my input signal and disrupting the supply to the FPGA. This might also explain why the FPGA was producing junk characters on the LCD. Here's what I'm referencing anyway:

@mjkuwp
I was initially. Considering what I mentioned above I'm still not sure how the ground along was introducing noise. There are obviously some other elements at play. I've replaced the original signal lines with some shielded cat 5 network cable and connected the shield to ground on the sensor side. Seems to be doing the job for now. Let's see how we go.