999 749/999s Swap – Vertical Cylinder Misfire & Exhaust Backfire At Steady Throttle

Discussion in '749 / 999' started by Brad_BNE, May 20, 2026.

  1. Looking for some advice on next troubleshooting steps for an engine issue with a 999S motor swapped into my 749 track bike.

    The bike runs, but has a noticeable hesitation/misfire, especially at moderate steady throttle. It feels much less obvious under hard acceleration or decel.

    I believe the issue is isolated to the vertical cylinder, as that appears to be the cylinder backfiring through the exhaust (see video).

    Setup:
    - 2006 749 frame
    - 2005 999S deep sump motor
    - fresh valve shims with MBP retainers
    - new timing belts
    - 2006 999S map (shoutout to member - the_jackal)
    - also tried a DP map with no improvement
    - Stock headers with cat removed
    - Original muffler cored with straight-through pipes + H-link
    - DNA filters
    - IRC quick shifter (currently disconnected to eliminate it as a possible cause)

    Parts replaced during troubleshooting:
    - fuel pump
    - fuel pressure regulator
    - fuel filter
    - coils
    - spark plugs
    - ECU (848 5AM HW610 flashed with 999S map)
    - 999S airbox and throttle bodies
    - TPS
    - added second engine ground strap from battery to motor

    Troubleshooting already performed:
    - verified timing belt alignment and tension
    - swapped CPS from original 749 motor and shimmed to spec
    - swapped coils between cylinders
    - swapped plugs between cylinders
    - swapped injectors between throttle bodies
    - tried multiple maps and reset TPS after each flash

    At this point I’m trying to avoid continuing to throw random parts at it. Curious what experienced 749/999 owners would check next.

    Any suggestions appreciated.

    https://youtube.com/shorts/iT9149bhYWI?si=wp9TR5Xha9V727nc
     
  2. Bump. Any ideas would be much appreciated. Thanks!
     
  3. Compression test when cold, and another when warmed up?

    Have you tried a stock exhaust?
     
  4. It appears to be only popping from one cylinder. Left as looking from the back of the bike. Does this swap if the coils are swapped over? Post the reference of the map flashed to the ECU.
     
  5. I'm not sure this presents an equal exhaust restriction/back pressure to both cylinders.

    Which considering everything else you've covered, could be your issue.
     
  6. Thanks for the response. I’ll do compression tests both hot and cold this weekend and update the thread with the results.

    I do have a stock can (which contains the cat for the vertical cylinder), but not a stock header with the horizontal cylinder cat. I’ll throw the stock can on as well and see if anything changes.

    Out of curiosity, given both exhaust paths are essentially straight-through right now, is there any reason you can think of that only the vertical cylinder would be affected?

    For further context, I previously ran this modified exhaust/can setup on the original 749 motor and it ran great, although that was with a Rexxer map.
     
  7. Yeah, just the vertical cylinder. I have swapped coils between cylinders and installed a completely new set of coils and behavior is the same.

    ECU files I've tried:
    221999SDQDP_5AM_Ducati_2005_999S_57mm_DP
    999S-2006-28640841M-IAW5AMHW610
     
  8. Thanks, like 'The Royal Maharaja' suggested, I'll put a stock can on and try that, although I don't have a stock header/mid-pipe so it will be heavily restricted on the vert cylinder and not on the horizontal (given cat for the horizontal cyl was in the mid pipe, yet for the vert cyl, it's in the can).
     
  9. Your set up is more in line with the slip on DP than the full system DP. I would try flashing 96510603B for the slip on. The full system has the banana pipe to balance the 57mm system.

    Hopefully it is just a fuelling issue on the vertical cylinder due to you running the full system mapping.

    221999SDQDP_5AM_Ducati_2005_999S_57mm_DP = running rich
    999S-2006-28640841M-IAW5AMHW610 = running lean

    Both will cause popping and flames due to unburnt fuel. The long horizontal link pipe probably gives some balance, hence why the problem manifests itself on the vertical cylinder.
     
    #9 chrisw, May 28, 2026
    Last edited: May 28, 2026
    • Like Like x 2
  10. Also, Ducati/Termignoni engineers spent time and research developing their exhaust systems. The horizontal and vertical link pipes for the 57mm systems are actually identical in their volumetric capacity despite being different in length.
     
    • Like Like x 1
  11. Thanks Chris, yeah I know the system isn't ideal the way it's modified. I'll try get my hands on the 96510603B/slip on map. If no joy, I'll try find a proper exhaust system that's not crazy money. Thanks for the advice.
     
  12. I think I can send you this map, but not home till Monday.
     
    • Like Like x 1
  13. Sorry for the slow reply. I'd really appreciate it if you can send me this map file. I had a look over the weekend but couldn't locate a copy. I'm in no rush so whenever you get a chance to look for it, that would be great. Thanks!
     
  14. Hi Brad, I'll have a hunt, but I'm travelling again so it will be Saturday at the earliest.
     
    • Like Like x 1
  15. Thank you kindly. No rush at all - I appreciate the help.
     
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