a little theory on the the radiator cap...as the value in pounds increase relative to the pressure rating of the cap...so does the temp in which it would take the engine to boil over. You would certainly know if the engine boils over as you'll smell it and most likely see some smoke. You should also be able to smell coolant under the hood on a hot day if you have a serious leak.
On the water pump...yes if its not leaking and not making noise and not the OEM pump, then I would leave it alone unelss you can't rule it out.
I saw a thread where the guys on the 80 section with SC were griping about the TRD fan and where Dan at american toyota had alternative known solution.....some other radiator fan will replace that one...
job one... have teh coolint system pressure tested? The only thing about the radator cap is that one...it should be the proper cap to fit the radiato as to allowing the coolant overflow tank to work right and two it should be the proper design, as in the proper lbs rating. Check for oil in the collant and coolant in the oil just as a precaution.
If I had a SC 80, the fan clutch would have the "thick" fluid in it that some of hte guys out in the desert run. THe idea there is that teh thicker fluid makes the fan clutch work harder...or really not slip so much. Yes it will make more noise, but cooling issues would generally go away.