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Make sure they are tight. Check all of your ground cables and make sure they are all secured. Look for corrosion, cuts, kinks, etc... If they all look good next is to check they are good.
Do you have a DMM? You can check for voltage drop. Place one lead on the positive terminal, and get a voltage check before starting. Once you have the battery voltage start checking all of the ground locations for voltage. It should stay the same. This includes checking ground on the vehicles body, the engine, or anywhere else you see metal. If that is all good. Have someone crank the car and check voltage while cranking. It can drop a little, but you don't want it to drop bellow about 10 volts.
 

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I doubt it is the coils or plugs. They don't fail like that. Do not throw parts at it. Pretty much everything is checkable. Since the battery was the last thing to be replaced, that is the first thing to look over. Who installed it, why was it installed?
 

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Since your only issues are misfires, I'm going to rule out air, or gas. They usually are accompanied with associated codes. Same with EGR. I'm thinking electrical. You have ruled out timing belt, and sensors would pick up on that. The misfires are both heads, and so it isn't associated with one head. I'm not thinking it is internal engine issues.
Another easy thing to check is Serpentine belt, especially if it was making noise prior. It could be dragging. I don't think it is valve lash since they don't fail together like that. You would have had issues with a single maybe 2 cylinders.
Have you checked your fluids? Transmission will be hard to check since it has to be done at operating temperature, but check your engine oil and see if it is low. Do not add transmission fluid since it will show low cold.
I'm thinking wiring issues.
 

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You can check the battery cables for resistance and voltage drop as well. With the DMM attached to the positive cable, attach the other lead to the end of the positive cable. The cable to the starter is fine as it is starting the car, and won't effect the car once started, so check the cable leading into the fuse box. You have to put it under load, so have someone crank the engine and check that there is little to no voltage loss. You will see the voltage spike if it is losing voltage. If you see no voltage loss, check the cable to the alternator. Same test. Same results, check the ground cable. Go to setting resistance, and do the same with the ground wire from the battery to the chassis. You should see very little resistance. If it spikes you found your wire. Your battery could be bad too. Even though it is new, doesn't mean it is good. Especially if you went with a bad brand, or they sold you an old/used battery. I go with Walmarts Everstart Maxx. Works great 5 year warranty. Check the case of the battery. Do the same test with the DMM one lead on the positive, and start touching the case of the battery with the other lead. If the case is dirty you can get voltage drop through the case. Corrosion on the terminals can also cause voltage drop. You want to keep these things clean so the power can flow through the system and not into the air.
 

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Rocky good advice, but never check or re-gap iridium plugs. You don't even want to touch them. Visual inspection is advised. A gap issue can happen if the plugs were dropped into the spark plug tubes. Otherwise gap shouldn't be an issue. Another thing to check with the spark plugs is that they are NGK or Denso. Nothing else should be in our engines. Plugs should be bought from a reputable source, not Ebay or Amazon, or other sketchy website.
 

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Rocky do you drive short trips? The cats fail if they don't get up to operating temperature. They only work hot. If you live in an area that doesn't have high speed roads like freeways or highways, that would explain your failed cats. Otherwise they can survive the life of the vehicle under the right conditions, or last years if they never actually get to operate.
 

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newer Honda engines don't have this as the drive-by-wire throttle body controls the idle.
might try cleaning this part first and see if vehicle operates any better then probably replace it for a longer more permanent solution
There is a cable. It goes to a box on the passenger side firewall up top. You will see a black cover and 2 or 3 bolts I forget how many holding it on. Remove the cover and you will see the cable. Then wires go to the Throttle Body from there.
 

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Thought you were talking about the newer vs older 1st generation. Not newer generations. I also thought I was responding to the question about cable slack in another post. Just realized this is a completely different thread, so your post made different sense to me, and was a little confusing trying to figure out what you were even saying in your post. lol. It all makes sense now.
 

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Where are you getting fuel smell from? The fuel enters the rails from the 3rd injector site. Another hose feeds the front rail. I wonder if it is reaching cylinder 2 and 3 and losing pressure by cylinder 1, and losing pressure on its way to 4, 5, 6. If you smell fuel in the engine bay, that isn't right. The exhaust yes, but the engine bay, no.
 

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The surge is Idle Air Control Valve. The shaking is likely related. Remove the Throttle body and clean it really well. Do not move the Butterfly Valve. I would say clean it without removing the Throttle Body, but I bet the gasket is bad. Replace with a new one, and make sure to get the old off. Do not scratch the aluminum surface. You can use a plastic razer blade sold at Walmart. Make sure to dry it before re-installing it. If you don't the liquid-carbon created from cleaning will dry and cause the butterfly valve to stick, or could settle at the bottom of the butterfly valve and cause it to restrict airflow.
Razer blades
 

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If you have a quality vice grip, you can get on the screw head from the side and twist it off. If you made a good cut on the screw head you can also use plyers or something similar on the flathead to help twist the screwdriver giving you more leverage.
 

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There are two different types of impact drivers. Both have flathead bits. The hammer style that you hit can even take a socket depending on the style. The electric impact driver would work as well.
 
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