I pulled my engine/transaxle on my 99 RAV4 4 door and I while it was out I did a total rebuild of the cooling system. My original radiator was badly clogged and the fins on the lower third were badly deteriorated, so I replaced it and the other following components:
Spectra Premium CU2292 Complete Radiator - Amazon.com
Motorad 2014-170 High Performance Thermostat - Amazon.com
2 ea - Upgr8 Universal High Performance 12V Slim Electric Cooling Radiator Fan With Fan Mounting Kit (14 Inch, Black) - Amazon.com
Gates TCKWP199BH Engine Timing Belt Kit with Water Pump - Amazon.com
Gates 19050 Heater Hose - Amazon.com
Gates 19051 Heater Hose - Amazon.com
Gates 22381 Lower Radiator Hose - Amazon.com
Gates 22382 Upper Radiator Hose - Amazon.com
Bypass hoses 1, 2, and 3 - local purchased
DNJ ENGINE COMPONENTS FPS907 Set; Freeze Plug, Brass; Freeze Plugs - Rock Auto
Oil system - while often not considered part of the cooling system, oil actually accounts for about a third of your engine cooling.
DNJ ENGINE COMPONENTS OP940, Oil Pump - Rock Auto
24K Gold Aluminum Oil Filter Relocation Male Fitting Adapter Kit 3/4X16 , 20X1.5 for Toyota MR2 - Amazon.com see link Installed a Oil Filter Relocation Adapter Kit
A word of warning to prevent future corrosion problems I would highly recommend using a quality antifreeze mixed with distilled water at 50/50. Don't use tap or well water in a cooling system because of the metals and chemicals that can and will cause problems. Even if your coolant is rated at 5-years, replace it at least every two years, as coolant becomes acidic and therefore corrosive with age.
To aid in cooling and corrosion control, I performed the following on the block, heads, intake manifold, transmission:
Degreased
Washed with Dawn dishwashing detergent
Wire brushed
Wiped down with acetone
Wiped down with denatured alcohol
Primed with very high temperature primer
Painted with very high temperature paint
Forgot the radiator cap.
Motorad ST-36 Safety Lever Radiator Cap - Amazon.com
I used 3/8" fuel line for the hoses going to the throttle body from the evap cannister
I also used 3/8" for the hose going to the back side of the heads, that runs just over the top of the fuel injectors.
The only thing I didn't replace was the heater core but someone that owned the RAV4 before me must have replaced it not too much before I bought it. I flushed it before I hooked it into my new system and the water was very clear right from the start, I rinsed it out with distilled water and hooked the heater hoses up.
Filled it with Prestone Anti-Freeze, 70% and 30% distilled water. I did not use extended life anti-freeze as it gets acidic after a few years and must be replaced anyway.

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