Now for the transmission cooler, there is two hoses coming from the trans, up to the front of the radiator, going into a black mesh looking condenser thing. It's two individual pieces mounted to the radiator....
Sounds like you have an external transmission cooler (separate from the radiator). You could use light water pressure to clean it off, don't "scrub" it or anything, you don't want to damage it. Since it's a separate cooler, this is almost certainly not causing a hot engine.
You also most likely have a power steering pump cooler in the same area in front of the radiator, I bet if you trace the lines from the power steering pump they go to another external cooler.
Sounds like you have a good thermostat (stock is 195 deg F by the way). If you used an oem replacement from autozone that should be fine. A 180 thermostat is a good idea, but is not the fix for your problem, something else is going on.
Sounds to me like you have a newish, clean, and not clogged radiator.
Also sounds like you have a new water pump, which is almost certainly not defective (although possible that it could be...).
Your heater core sounds like it may be clogged. This won't affect engine overheating though.
If your radiator hoses are not clogged, and the engine does not have a clog in it, then you must have air in the cooling system.
Also sound like your clutch fan is good.
Did you purge the air out after refilling the coolant? Air in the system will definitely cause sporadic heat spikes. You need to park the truck so that the radiator is the highest point(put it on a slight incline, or jack the front up a few inches). Then remove the radiator cap, start the engine, turn the heater on, select the floor vent setting, put the fan on high, and make sure the heat is set to HOT. Then monitor engine temperature let it get as hot as it will get (to operating temperature). While it's running you can "hit" the radiator hoses or squeeze them to try to dislodge any trapped air. At some point the thermostat will open (at about 195 deg F) and water in the radiator should go down and enter the engine. You can then refill the radiator to full, then fill the expansion tank to full, replace radiator cap and then after a few heat cycles of running the truck you may need to add a little more coolant again.