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Rebuilding 90 civic Hatchback having Issues


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Alright I'm rebuilding a 1990 Honda Civic Hatchback with my Uncle. This car was mechanically messed up from morons who had the car before me that half did everything on the car. My uncle is a genius at rebuilding these things but he's been incarcerated and now it's up to me to finish it and i'm getting a bit lost. Shortly after swapping the intake manifold from a 2 injector to 4 (the people had it vice versa for more gas mileage...) the idle started to pulse whenever the clutch was pushed in or the car was in neutral. I thought this was because of the cold weather but we've had some hot days back then and a few days ago and it's doing the same thing. At first a Mechanic suggested vacuum leaks in the intake, we found a hose got mixed up and and we did indeed have a vacuum leak. The intake was completely sealed up and the car ran great for a month or two tops. I'm again having the same pulsing idle issues. At night driving home the headlights pulse with the idle and the car hasn't died from it but it just sounds like hell! I'll pull into the driveway, play around with the heat switch, In-car light, Radio and the headlights, any combination of flipping these on or off including bright lights will eventually get the idle to stop pulsing. I've talked to 4 mechanics and all are saying something different and I'm to the point I feel none of them really know. The only thing they had in common was a possible Bad Ecu. Anyone have any idea what is going on and what I could try to fix it?

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The Check engine light is on, we've checked the code it's the EGR valve which was pulled out and sealed off by the former owners. It does drive really well. I'm still learning what all my uncle did we did rewire the engine harness. I figured it was multiple problems one mechanic suggested the trottle cable, there are some cuts in the cable it's possibly sticking and the Loop isn't tight enough is all he told me. I'm assuming that's the Loop from the firewall around to where it connects on the trottle body?

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