1) The discolored oil on the bottom of the oil cap means NOTHING. That can be condensation from the engine going through dewpoint and moisture condensing on the bottom of the cap.
2) What color is your engine oil? If it looks like chocolate milk, do not run your engine. That means that the coolant has mixed with the oil and coolant does not lubricate well (forget about the synthetic comment above)
3) As
@NLXTACY stated above, once the thermostat opens, you will see coolant flow in the top of the radiator. It will go from LEFT to RIGHT when sitting in the truck.
4) You coolant should be red or green, not brown, orange, or otherwise. If red and green have been mixed, you will get a brown sludge with a greenish tint.
5) Your entire cooling system only holds about 4 gallons after a complete drain (even pulling the plug in the side of the block). How much water did you add?
6) Definitely change your oil and do a Blackstone analysis on the oil pulled out. That will pinpoint it if there is a problem with the HG failing and getting into the oil.
7) After you refill the radiator with water and run it, as it warms up, the coolant will expand and may overflow your radiator. That's OK except it makes a mess. Short fill it about 1/2" to help allow for that. Fill the radiator, then park with the front end up on ramps or very uphill with your heater slide on "hot" in order to circulate the coolant and eliminate the air bubbles. This may take 3 or 4 cycle times to complete. I filled mine with the front up, then drove it around and parked overnight with the front uphill. I rechecked in the morning and did the same again. It took 3 times for mine to stay full.
8) Make sure you install a new radiator cap from TOYOTA. The aftermarket ones don't quite fit right and may not be set properly for the pressure. My old radiator cap was clogged up on the spring and would not relieve, causing my radiator to explode after a sudden heating event.
9) If it turns out you do have the sludge, I would just purchase a new radiator rather than having your old one rodded out. The plastic top on these are known to fail drastically due to numerous heat cycles. (A new radiator comes with a new cap) New radiator is $385 +/- from CDan.
Good Luck!