Harley Intake Seals

Q: Sorry this is so long
Bob & Mark,

I love Fix My Hog! I tell all of my fellow Harley heads about it and they’re extremely impressed with the work that I’ve done on my bike. They jokingly call me wrench now. You might remember me I changed my cam tensioners and installed adjustable push rods. I just installed a 3″ tank lift, a new clutch pack, inner race spacer, inner race bearing and a new starter pinion gear. My bike is now completely reassembled. I have decided to take on another project that I’ve noticed ever since I got my bike. It seems more noticeable now that the other issues have been addressed. For the first 30 minutes to an hour my bike runs like a dream. The throttle is hyper responsive and it GOES! However, after it gets up to normal operating temps you can clearly feel that it’s running rough. The vibration of the motor seems shake the bike harder. The throttle is no longer responsive. It feels like it’s slightly misfiring and when I shut her down it takes a really long time for it to cool down. Mechanics at Harley have given it test rides and are telling me it’s fine. They say Dyna’s tend to run rough and so on. However, my little brother has the exact same bike and his doesn’t have this issue.

I’ve consulted the trouble shooting section of my manual and have done a bunch of research on the internet. I have found (5) possible diagnosis. I have listed the down below and have attached a couple pictures. I think I ruled out the first one by priming the fuel pump, pulling the fuse and firing the motor. I’ve also started the bike with very low fuel and still runs really well until it get’s hot.

1) Pin Holes in fuel lines

2) Fuel Injector Wire – I read somewhere that if one of the fuel injectors has a bad wire it might operate properly while the wires are cool, but as they heat up and expand a bad wire may be exposed and they may begin misfiring. Is there a way I can test these?

3) Excessive Carbon on Piston Heads – (I have attached a photos) When I had my pipes off I did a superficial inspection of my piston heads with a flashlight. You can clearly see that my pistons have a thick layer the carbon all on them but they also look like it is worn really evenly which my manual says is what I should like to see. How do you know if the carbon is excessive?

3) The engine temperature sensor -Is there anyway I can test this to see if it ‘s functioning properly?

4) Loose pin or bad connection at the ECM – Any Test procedure for this?

5) Bad coil – Test procedure?

Is there anything else I should check? Is there a certain order I should check this stuff in. I want to do as little work as possible so I can get in the wind! My bike has a stage one Screaming Eagle Air Cleaner, Vance and Hines Big Radius Pipes. My O2 sensors have been bypassed. I don’t have a fuel pak installed and it has never been dyno tuned, but I do have the Harley Stage 1 download. Thank you for everything!

Brandon K

A: Brandon, what you describe sounds more like a tuning issue than a sensor, or mechanical malfunction.

But, here are a few things that come to mind:

Check your speedo for trouble codes.

Check for an intake leak: When a bike has an intake leak, it will run differently from cold to hot. If the Harley intake seals have not been replaced on this bike yet; it may be time.

Electrical Manual: Pick up the electrical manual for your bike. Someone like yourself can really benefit from this book. There is an enormous amount of valuable information packed into these manuals. You can learn how to test every electrical function on your m/c.

This is invaluable when trying to narrow in on a failing (or, intermittently failing) sensor. A bad sensor will often fail when the bike is hot.

If you find yourself running out of items to test, you may want to schedule a dyno session.

Related Video: Intake Seals
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7 Responses to “Harley Intake Seals”
  1. JP

    Swap your ECM with unit from your brother’s bike. If this resolves problem and symptom shows up on brother’s bike you will have solved the problem. I’m suggesting this because a friend of mine had a similar issue which got resolved with a new ECM.

  2. Rod Fleischman
    Rod Fleischman

    Most of the videos are on old bikes. That’s fine as far as it goes, but the newer bikes have some different issues, such as hydraulic clutch and antilock brakes. I would like to see some of those topics covered.

    • Dennis Santopietro
      Dennis Santopietro

      Hi Rod, I’m not sure of the question here? We have videos covering 1984 through today’s Twin Cams. We show brake service on the Brembo ABS calipers and more. Give me a ring if you need help finding something. 619-269-9321 Wrench Safe, Dennis

  3. Mark Jirjis
    Mark Jirjis

    I had very similar problems on my 95 ultra, Intake seals were shot , also had to reset hot & cold Idle & runs great now !!


      How did you know your seals were bad?
      What did you have to do to reset your hot & cold idle settings?

  4. Len

    Just tossing this out there. How bout the engine temp sensor? Cold engine has a richer fuel mix. Is it possible the motor is running too rich at normal operating temp due to a bad sensor?

  5. Peter Fox
    Peter Fox

    Engine choofed a couple of times if i didn’t allow the engine time to fire, changed the inlet “o” rings on the fuel injection. Starts first time everytime and it used to sit for long periods of time up to my recent retirement. Cheers Foxy of Geelong Australia.