Apologies in advance if something like this has already been posted.
1999 Honda Civic Ex. 145,000 miles on body, 15,000 miles on rebuilt motor.
I started it up one day and it idled high and then immediately after it started misfiring and running like garbage. First codes were cylinder 1-4 misfire along with random misfire. I took it to my trusted shop and they were able to verify that whoever rebuilt the motor did not tension the timing belt correctly. When it was running like garbage it was making this intermittent clacking kind of sound in the top end at idle. He installed a new timing belt, adjusted the valves (said they were a little too tight), and set the timing properly. Its running great however it is now randomly jumping to about 1800rpms at idle and making the clacking sound consistently upon idling back down. New code is for Vtec system malfunction and it has the tiniest misfire when it does the idling/clacking thing. It is also rev limiting at 5,000rpms and he said he cannot get the ignition timing quite right and thinks it is possibly related to all of this. We have also verified it is not the distributor, cap, or rotor. I appreciate any input. We are going to try a new Vtec solenoid but I'm curious if anyone has experienced this and it was a different problem for you

 

Sounds like a bent valve. Timing belt being loose could cause issues, including the cam gears jumping teeth. There's a good chance a valve went down when a piston was up and bent it slightly.

 

I would’ve thought that initially but it’s not consistent with revolutions. It’s at the point where it only does it for like a millisecond upon idling back down. Otherwise it’s completely silent and no power loss. I’m by no means a guru but wouldn’t be a consistent clatter if it were bent enough to make the noise?

 

Also it only jumped a tooth and it did it at idle which I know his highly unlikely to cause any permanent damage like that. Definitely not saying it’s impossible though

 

Only 1 way to find out. Pull the head and inspect the valves.

 

Try a Leak down test to see if the valve may have bent.

 

Fix the VTEC code and then go from there.

You can't set the ignition timing properly until the engine idles correctly and vice versa. Return to this after the VTEC code is fixed.

 

Is it possible that something in the distributor is minutely causing this issue? My mechanic says he can watch the ignition timing fail every time it idles back down and clacks for a second. Its the original Honda distributor and I know they don't last very long. It may also be why its rev limiting at 5k?

 

Are you looking for us to pin point the issue over the internet on the first try without seeing the vehicle in person? Sounds like our suggestions are going in one ear and out the other since you haven't bothered trying any of them. Do a leak down test. This will let you know if there's a bent valve. With the timing belt jumping a tooth or two, damage can be done without you even knowing. The slightest bend will cause issues. If everything comes back great, then try a different distributor. If the problem persists, find a mechanic who knows what he's doing.

 

My best friend bought a car with a wiring nightmare. Car ran good and when vtec engaged the car would cut power and bog then throw CEL. It was a non vtec car to begin with and when the throttle position sensor was wired from 4 wires down to 2 wires and they were the wrong two wires. Worth checking that because it sounds similar. Would definitely do the leak down test first to see if it's a bent valve.