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Just picked up a well-used (35,000 miles) fully stock (except for K&N air filters) 2006 S2R800 that has probably never seen a Ducati service. Previous owner said it was running fine (lol) but this thing crapped out on me the day I bought it. Took it to the nearest Ducati mechanic who, for $700 got the thing running again (apparently an electrical fault was keeping it from operating both cylinders; it was fouling the sparkplugs and not holding idle). It ran great for a few days, now it's back to stalling, rough starts, surging and overall lousy running. Not a viable machine and the best the mechanic can tell me is that I bought a bike with too many miles on it and that nothing will be right until I spend $1500 for the big service. I get it - it needs the belts replaced and the clearances checked. But this issue is bigger than that.

I've got a 2003 Honda CB919 with almost twice the miles on it and that bike is bulletproof. Starts up every time and runs perfectly all day, every day. I'd welcome any feedback, because right now I hate Ducatis, and I don't want to! When it was running I enjoyed the bike. What is up with this thing? It seems to have very poor fueling behavior. Not helpfully the mechanic let me know that later versions had better fuel injection. Again, my older Honda hasn't had a misfuelling or misfire since I brought her home 8 years ago.
 

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Check all the usual culprits.
The white plug between the generator and rectifier.
Replace fuel filter, check the lines inside the tank.
Try to flush the fuel system.
Open and inspect/clean all the electrical connections you can find.
If it hasn't been looked after it probably hasn't been mapped to suit the K&N. Maybe put a standard filter in it.
Same thing for after market exhaust if it has one.
The biggest issue with ducs is that people get problems and don't get them sorted out and then it develops another problem so you don't have simple symptoms to check.
You want to find a good mechanic who actually knows ducati and some dealerships don't necessarily fit this description but you really want to go over the basics before you take it in to cut your costs down.
The service is a big issue as valve clearances are critical due to the "desmo" set up. If a valve isn't closing properly it won't run properly and could be on the verge of hitting a piston.
Belts can slightly stretch which will put the valve timing out a little bit.If a valve isn't closing properly it won't run properly and could be on the verge of hitting a piston.
Have you replaced the spark plugs?
My S4 is well set up and runs great but 15000 kms after a service and it started stalling at the lights, new plugs fixed it.
Youre right about the jap vs duc relability/servicing.
Pull your seat off, lift the tank and start at the air filter case and start cleaning/checking stuff and look for silly issues but the service could be the main issue.
A major "ducati service" will, depending on milage include stuff like brake pads, chain and sprockets, replace fluids including fork oil.
Always talk to your mechanic and see exactly what he is going to do and get him to just concentrate on the engine but most importantly find a mechanic who actually knows ducatis.
 

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i would bet my last $10 on the belts. do not worry about going forward and its a super easy job to do. i own a s2r800 and its not anywhere as finicky as other models. and you do not have to pay as much attention to service as the more complex liquid cooled 3 or 4 value bikes. the 800 is a most basic engine with fewer parts to go wrong. its a lightweight and lives in a much lower rpm rate.
its the single sided swingarm that kills chains sprockets and bushings. not the ducati
i do my own work. the 800 bike does not require a ducati specialist like other models.
yes valve clearance should be checked about now. it is easy enough on our bike. most important thing is not to drop anything . and the collets are wee so pay attention. At 35000 your bike is really only just broken in. expect over 75000 and its unlikely that they will be far enough out of spec to be an issue on a 800cc aircooled.
if you are not already. facebook has a s2r800 1000 only group that i help manage. join us.
the only horror show you are gonna have is the dumbass smile you are gonna get once this is behind you.
 

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Firstly, I would be asking the mechanic, exactly what he did to get it running. What was wrong? All 700 dollars worth of information.??
maybe it would gives us a clue, did he do it right, or just mess with something that now is going wrong again, what was replaced? etc.etc.
Pull the plugs and see if it's back to fouling.

I have owned Ducati's for many years, I have 3 times more miles on my old 900ie. never lets me down, and runs just like your Honda.
Sadly, all machines can break down, buying second hand is always a risk.
 

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I love my S2R 800 with the same mileage as yours. It wouldn't idle without the throttle switch thing when I bought it, but I was lucky enough that swapping around the valve shims was enough to get things in spec and adjusting the throttle body balance was easy. Changed the belt for good measure. After that, it's been just great, though I should probably change the friction plates. Only thing I'd want different is an extra 200cc and the dry clutch.
Stick with it. If even I can service mine, you should be good to go.
 
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