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I have ran in to this before as an engine performance and emmission technician. Sounds like the problem is in the brake booster area is leaking vacuum (air) in to the engine causing a major missfire due to a lean condition. The best way to check this with the engine off and cool so you dont burn your hands. Remove the big vacum hose that goes up to the brake booster and plug the vacum port to the engine. Make sure you get a good seal on the plug and no air is sucking down when engine is running. After that start the engine and make sure it is running smoothly, apply the brakes and see if the engine remains running smoothly. 99.999% of the times the issie is with booster tht when you apply the brakes you allowing vacuum to leak in to engine. Replace booster and hose with new, do not go to junk yard . By tge way the brake pedal will be stiff because it needs vacuum to make smooth so dont alarm your sekf while testing it. Good luck and let me know what happens.
Believe it or not the firing order is 1-2-3-4-5-6 The cylinder locations are 2-4-6 in front by radiator, and 1-3-5 against the firewall. If you have a misfire on a certain cyl. and you've replaced the plugs,wires and cap and rotor, you probably have a fuel injector that's dead or plugged,it's common on Quests. Figure out which cyl. is misfiring and unplug the fuel inj. conn. with the engine running and listen for a change in RPMs. If there is no change then replace the injector.
make sure the firing order is correctly. going clockwise on the cap it should go 1-6-5-4-3-2 and the cylinders are numbered as follows: passenger side from front to back is 1-3-5 and driver side front to back is 2-4-6