the wife is driving the civic for now, and I sweat too much to bike to work in the summer
Get another one. This is 2011- the time for solo commuting in pickups should be well behind us now.
I'm under the impression that the cooler thermostat helps get the engine out of open loop faster, thus decreasing the amount of time the computer forces the engine to run rich in order to get to operating temp.
That's bass ackwards.
I wasn't clear about the pump, I meant electric water pump, not fuel pump.
Forget that.
I don't do any offroading, so extra ground clearance (up to a point) isn't worth anything to me. Currently I have the truck leveled (lifted about 1.5" in the front) but I'm learning that this twin i-beam axle in the front is a real pain to get aligned at non-stock heights, so I'm giving real thought to putting the stock height coils back on the front and putting a smaller block in the rear to make it sit level (non-level truck is a pet peeve of mine).
Go stock- a bit nose down is more aero.
I am interested in the idea of an air dam and/or underbelly pan but I worry a bit because my understanding is these trucks are bottom breathers... with a full or partial grill block and an underbelly pan, will the engine be suffocated?
I run a full grille block AND no fan AND engine blanket (but I have to pull the block out in summer when towing). I'm making an air dam too (search for my thread) but don't know the effects of it yet.
Frank keep in mind the truck is not at 100% right now... if you look at my fuel econ graph, the upward trend you'll see is due (at least in part, imo) to the ongoing repairs being done on the truck. I think once I replace/upgrade the plugs/wires I'll see another little bump in fuel econ, and replacing the differential fluids with synthetic will help as well.
Seriously. If you aren't hauling/towing, that thing outta be parked. 
P.S. 5 miles trips, 45 mph, cold both directions- that's way more of a problem than aero. Grille block and engine blanket and fan delete- same stuff as mine will get that thing into closed loop much, much faster. Make sure there are no dragging brakes- I've had to free mine up.