Thanks for the tips but with the current plan - neither are really feasible.
Because the foot control only goes from 0 degrees to 360 degrees, its most comfortable to have halfway be at 180 degrees (straight forward). If I rotate the shaft to where the cable is out of the way, I have to heel all the way down to toe all the way down to veer slight left vs slight right. Not ideal.
Heres another picture with it in place and a couple more pieces of carpet. The picture doesn't really show the depth right, but it almost comes out to my knees. Its functional now, just not comfortable. Still, not quite enough room to not have the pedal cover up one of the hatches. Should have bought this thing before I started the framing & decking. I'm going to take it out Saturday for the first time and see how much it bothers me when I'm actually fishing and not being critical in the garage.