All 4th Gen 4Runners take Toyota SLLC (Super Long Life Coolant), its a Non-Silicate, Non-Amine, Non-Nitrite and Non-Borate coolant with long-life hybrid organic acid technology.
There are some alternatives like Zerex Asian Formula & Amsoil Coolant that meet Toyota's requirements. I haven't be able to verify many others that actually meet all of the SLLC specifications.
You've contaminated your system with the incorrect coolant by placing a generic silicate coolant in your vehicle. First I will recommend that you find if there is any leaks causing your coolant to go down. You did not state what engine you are running, but it is not uncommon to see water pumps leaking on '04 4Runners with either engine.
After you've corrected the coolant leak (if there is one), I would recommend a good coolant flush with Toyota SLLC or equivalent coolant. (Mixing Toyota "Red" LLC- Long Life Coolant with water does not make SLLC)
Toyota SLLC:
Amazon.com: Toyota Genuine Fluid 00272-SLLC2 Long Life Coolant - 1 Gallon: Automotive
Zerex Asian Formula:
Valvoline.com > Products > Zerex > Antifreeze Zerex > Zerex? Asian Vehicle Antifreeze / Coolant
Amsoil:
AMSOIL Antifreeze and Engine Coolant