Going standalone isn't going to be any easier; You'll still have to replace the wiring harness then diagnose and replace any bad sensors (and replace any that are incompatible)... With some setups you'll need to add additional sensors and make modifications to mount them (such as a crank position sensor). Then there's tuning, the cost of adding a wideband (if you want reliability and on-board tuning). The easiest to install standalones use the stock wiring (ie: AEM and Apex'i).
Most wire harness failures are located at or near the connectors or in high heat locations. If you have recurring error codes they'll often point out the most likely suspects. The wiring which passes over the engine (AFM, CPS, oil pressure, temp sensors and O2) are the most susceptible to heat damage. Testing the wiring for voltage drop is a simple procedure once you get the hang of it.
If you opt to get a replacement OEM harness you may find that Toyota no longer has them (probably not too bad as you would then find out they ran around $500)... There is an established wire harness company who has added replacement 7M wiring harnesses to their product line, but I can't remember who and don't know what the pricing is. Personally, I just rebuild them myself, but it's time consuming and getting replacement clips is sometimes a pain.
No error codes coming up?
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