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Whilst all the advise on fuel, battery, plugs etc. change are generally good and should be checked first, the earlier 749 and also the 999S all had stalling problems, especially with open exhausts. This can be traced to the ECU IAW59M. This is one of the reasons (there were other issues as well) that later bikes got the IAW5AM instead. It has among other things, different timing maps for the 749 to cure the stalling (and maybe also for the 999, but I can't confirm this). Your bike being 2006 should normally have the IAW5AM, but you can never be sure! Ducati is/was notorious for fitting whatever was on top of the parts-bin...

At any rate having a PCIII will not help the stalling, since that device only kicks in from somewhere between 3-4k rpm and doesn't modify the timing curves at all.

Solution: ditch the PCIII and flash your ECU with the Ducati Performance map from at least 2005 (they issued several flavours of those maps as well). You can find the DP maps for both ECU's. I found that even using the standard 2005 999 map in my 59M ECU on my 999S was giving better low rev running than the OEM 2003 999S map. The 2006 DP map totally changed things and now it runs like a dream! So there is hope, even if you would have the 59M ECU. If you have the 5A you should still flash it with the DP map that is specific to the later ECU. In both cases, you can sell your PCIII!
 

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Regarding the 998: Yes most likely, the 998 uses the 59M ECU. Playing with my 999 and the same ECU, I found that some maps would have no idle and totally stall, whereas the DP map is very sweet and fixes the problem (I have a full 57mm race system). They never used anything else on the 998 (AFIK). Hypothetical question: Would you be able to retrofit a 5A? Maybe...the 999 engine is very similar to the 998, but it would run using a 999 map, since there are no 998 maps for the 5A and you can't load a 59M map in the later hardware (big no-no, as you will brick your ECU). It would be an interesting test. And also, the 998 59M is worth more 2nd hand than the 999, because they are all "virgin" = immo function not active...can be plugged in straight in a 999, reflashed with a 999 map, and you have a "new" ECU, sans the immo problems. You can even enable the immo function using the red key and procedure...
 

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A PC1, 2, 3 or whatever - and similar piggy-back systems- are just that. Hacks. They plug in to the OEM system and try to fool it. And people spend dollars for those, instead of going to the root of the problem and applying the easy fix, which is to modify the OEM system with OEM supplied maps.

Besides, try as you may, a Powercommander will never modify the timing map. A reflash of the OEM ECU with the proper map will.

Any reflash or change of the maps should be followed by not only a reset of the TPS but idle tune (CO level). A number of software can do the TPS reset and idle tuning for free. Provided you only get the right cables and know how to use google a bit.
 
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