When I originally did mine I removed and blanked all three pipes but left the connector plugged in and had no problems at all.
The electronic pump injection pump has no parts on it to remove for the EGR, The mechanical pumps do it's a throttle potentiometer. So you can't do anything with the injection pump anyway.
Eventually I disconnected the valve and removed it and taped the plug to the rest of the loom again with no ill effects.
I used to get low 30's running 255/65/16 all terrains.
You may find that changing to a 1.44:1 Transfer box rather than the 1.22:1 standard Discovery box helps with economy on short runs with the larger tyres you are running.
I now have 255/85/16 Cooper ST's and a 1.44:1 T-box and still get high 20's on a 20 mile b-road (50mph typically) commute.
Mine is also a 1996 300TDi Auto with a winch, snorkel, etc although no roof rack. Also mine no longer has the electronic injection pump but a tweaked mechanical pump.
Pete.