Spoke with a fellow enthusiast

The bike still has trouble starting. It's not an air problem. I've ruled out fuel. Last part of the equation is spark.

On Wednesday I ruled out the battery and solenoid once and for all. Bypassed the solenoid, did a direct connect to the starter. Same result, so the solenoid isn't the problem. Connected the battery to a shop car charger/starter. Same result. Tried jumping directly off my car, same result. Battery is fine.

Other than an acute timing problem, the only two things that I concluded could be causing the problem are the ECU or the coils.

My friend Mark turned me on to Rick, another Ducatista with an 03 999. Just so happens he's also a Bimmerphile like me, he did tech work on BMWs, so he's adept at diagnostics and knows his way around a garage.

I spoke at length with Rick today. He also had a chronic starting problem with his 03. We went through the usual step by step process of elimination and arrived at ignition. He said that since I was able to connect and run the diagnostics with the VDSTS, it's not likely to be the ECU (good news). His starting problem ultimately was due to the coils, and I mentioned that my coil test indicated 800 milli-ohms, much higher than the factory specked 650 milli-ohms. Rick said he talked to a few Ducati mechanics on the mainland, including the respected BCM Ducati. Bottom line is that 999 coils do go bad.

During my research, I discovered that EVERY year from 2003-2006, Ducati updated the coils for the 999. That kind of shit doesn't happen unless there's something inherently wrong with the original design. I verified this coil succession by going to the dealer and standing over the tech's shoulder as he looked up the part numbers in the database. In the end, Rick suspected it may be a coil problem, and I concurred.

At this time, there is a set of 999 coils on ebay for about $10. I looked at it again, fortunately the seller put a large pic where the part number is visible. I looked it up and it turns out to be the outdated coils. ARRGGHH! So it's off to the dealer, I'm just going to fork out the $400 for some new coils. I really hope this solves the problem. The next step would be to replace the ECU, which I priced at $1800 at the dealer, or $1544 online.