Did it quit while the vehicle was running or it just wouldn't start? Is there any sort of smoke coming out the exhaust while cranking? You also state that you replaced the fuel filter. Did you replace the whole pump and filter assembly or just the filter? If it's just the filter then possibly the pump went. I have never worked on a highlander so am not sure of the layout but the engine just needs air, spark, and fuel to work. You know the compression is alright as they're all over 100psi. The next thing I'd check is to make sure you have proper air and fuel flow. My suspicion is on fuel as normally intakes don't just plug right away and you'll see a gradual drop in power and fuel economy. You say the spark is weak and that can prevent a...