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Discussion Starter #1 (Edited)
I figured I'd make a purpose built thread for this issue vs. piggybacking off of my previous again. The bike has never started up on the first try but the last two days I've tried to get it started it hasn't after multiple attempts. The engine has gotten a new battery (Yuasa YT12B-BS), new plugs (NGK CR9EIX - did not gap, measured at 0.028"), and new belts (107 and 105Hz H/V cyl). Last time I rode it was after the clutch rebuild, and I managed to stall it at a top of a hill twice. Roll started it both times after the battery felt drained in order to get it back home. Went ahead last week and bought a CTEK battery maintainer to not have to keep taking off the fairing to access the battery and be able to plug it in to a set of leads. Today with a fresh battery I tried maybe 7-8 times with no luck.

Things I can think of:
Air filters are the original when the bike was sold. The rubber was deteriorating while cleaning them, and the filter itself had next to no material within the fibers. It shouldn't block any airflow at all.
Cold start lever when cracked 1/8" in. used to work on start up, now no longer does. Slight twist of throttle doesn't help either. Most of the times however I try to start it without touching the lever or throttle.
I have two leads on the + terminal, and two on the - terminal. Looking at this upgraded ebay kit I see only 1 + wire, so I'll have to look again at the bike to see where this other one is going.. It also appears that the - cable for the starter is starting to corrode. The strands at the end are exposed and have a light layer over them, but no discoloration. Ground on the vertical cylinder looks clean and is tight.
Starter motor doesn't sound the greatest.
Backfires on just about every other attempt to start.
I've yet to test compression for the cylinders. I'll attempt to get this done next after removing the tank...
Unsure about last time valves were serviced.

I'm not opposed to eventually upgrading the cables, but I don't think that's my problem. My guess is the starter itself. I'll have to look through the service manual this week to find anything about this but I won't be able to work on the bike for the next few weeks either...
 

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I have a 2002 998 that had similar problems, but would eventually start. It was the battery cables. I took them off, cleaned them, and haven't had a problem since. Bad battery cables can cause all sorts of starting issues.

I also traded an R6 for mine and dont regret it for a second.
 

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remove the clutch cover and watch the clutch. i think you'll find it's not actually turning, just knocking back and forth, meaning starter clutch is rooted.
 

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Discussion Starter #4 (Edited)
remove the clutch cover and watch the clutch. i think you'll find it's not actually turning, just knocking back and forth, meaning starter clutch is rooted.
I can check this although I'm fairly sure it is rotating (clockwise I think?) and the engine sounds to be turning over however (esp. with backfire and exhaust tone).

However, if I'm wrong, would this be the next step to undertake: Repairing/replacing a Desmoquattro sprag clutch

From the short amount of reading I've done on this, it's best to replace all of the components?

edit: Found this invaluable video on the entire job. Next is to find part numbers and look up costs. I'll run over to the garage tomorrow morning start the bike from the right side to see if the clutch is slipping and the pressure plate fails to continue rotation.This makes more sense than a faulty starter.
 

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Missing some details... How many miles on the bike? When was the last valves check? Did you read ecu for diagnostic codes? Do you get sparks on both plugs? Are both injectors spraying?

The "always need 2-4 attempts to start" is concerning, should always start first try.

What happen if you roll start it with a topped up battery?

Could be the sprag but to me it sound like the ignition is off or its missing fuel/spark.

First step would be confirm both cylinders get sparks and fuel, and a compression test while you're there. And read ecu codes maybe it will tell you something.
 

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Discussion Starter #8 (Edited)
Missing some details... How many miles on the bike? When was the last valves check? Did you read ecu for diagnostic codes? Do you get sparks on both plugs? Are both injectors spraying?
I don’t have an adapter that can connect to the lead yet, I’ll have to look around for one possibly. The rest can be answered in my first post. Also, holding the left button while turning key to ignition did not change the startup at all.

The "always need 2-4 attempts to start" is concerning, should always start first try.

What happen if you roll start it with a topped up battery?

Could be the sprag but to me it sound like the ignition is off or its missing fuel/spark.
Not sure what the difference would be roll starting it with a full battery vs dead. To my knowledge there shouldn’t be.

I do not believe it to be spark related. The coils look fine, wires look fine, and they are 2 month old plugs. Unless they’ve been fouled out from all the non-start attempts I don’t see this as my issue.

I know it’s getting fuel, whether or not properly from the injectors is unknown to me right now. In a few weeks I’ll be able to rip off the front fairing and a snorkle to see inside.
 

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i had a 999 that, even after going through everything at a 20,000km service, would still crank endlessly, but not fire. a set of motolectric leads fixed it - only change made at the time.

i advanced the inlet cams on another 999 (early base cam model) and that made it a chronic non starter too - would crank, but not fire. i was thinking it might need more fuel on the start up table, but didn't want to head down a potentially pointless rabbit hole so just put the cams back where they were.

if it has any sort of starter clutch problem fix that first.
 

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we're talking about the starter clutch, or starter sprag, or freewheel, or whatever else you want to call it. not the clutch between crank and gearbox.
 

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For those of us that don't work on the 999 on a regular basis I've found the easiest way to check injector spray is to remove the left air tube (snorkel?) and the filter and you can watch the injector spray with a torch. I don't have to remove the front fairing, just the side fairing. If you have really had a gutfull, perhaps substitute the torch with a match..... :)
 

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The 999 I recently picked up had a similar/same issue around what OP is describing as well as what belter just mentioned.

Trouble starting exacerbated when cold. Backfiring when it did start. Smoke from pipes and air box from fuel due to excessive failed starts. Cold start lever did nothing to help and in fact mostly made it worse.

After checking for the usual suspects of fuel, fire, air, and timing I decided to go down the path of upgrading the cable leads. Starting seemed weak so I upgraded the battery and starter leads along with a lithium battery.

And when I say weak I mean it did not turn over quite as “peppy” as my 1198 or M1200. Upgrading the above and the Issue was completely solved. I don’t use the cold start lever at all to get her going. Even when I fired her up the other day and it was ~45 F out.
 

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Not sure what the difference would be roll starting it with a full battery vs dead. To my knowledge there shouldn’t be.
If the battery is discharged or weak you may not get enough voltage to power the ecu and get good sparks.

i would not discard the sparks because wiring and coils looks good. A coil may look good and be toasted. The ecu may be in problem. The crank sensor or tps could also be defect so you don't have sparks.

But seeing that your engine rock back and forth instead of turning it appears to be sprag clutch related.
 

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Discussion Starter #16
If the battery is discharged or weak you may not get enough voltage to power the ecu and get good sparks.

i would not discard the sparks because wiring and coils looks good. A coil may look good and be toasted. The ecu may be in problem. The crank sensor or tps could also be defect so you don't have sparks.

But seeing that your engine rock back and forth instead of turning it appears to be sprag clutch related.
The battery has never gotten to a state where the screen won’t come in or is dim. Always been fully charged when trying to start.
I might try the hicap leads first after looking at them again in the next few weeks.
 

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Ran over to the garage a few minutes ago to try and start it while looking at the pressure plate. It rotates clockwise without having to touch the throttle or idle lever. When I crack throttle open about 1/4 however, the engine sounds to lug ad then the pressure plate only bounces forwards and backwards.
Pressure plate rotate counter-clockwise when the engine run.

Did you inverted leads to starter?
 

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Discussion Starter #18
Pressure plate rotate counter-clockwise when the engine run.

Did you inverted leads to starter?
Hmm.. from the right looking at the plate I’m sure it was rotating clockwise.
I haven’t touched anything starter related at all on the bike other than battery and plugs.
 

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Discussion Starter #20 (Edited)
Tried to start it five times just now, and the battery was on the float cycle on the tender. First try it always gives a short sputter but continues to crank over. The other 4 start attempts all had a backfire at the start/middle of the attempt. Something that it has always done however is that after a few rotations, the starter will slow down to about 1/4 speed for a second or so, and then it will rise back up to normal starting speed. I know the sprag was brought up but it this sounds like a drop in power vs. a whirring of gears (unless the starter is indeed supposed to act like this on a full, no-start cycle). I do hear a whir however at the end of a start cycle after the starter cutout, but it is only for a brief moment. Not opposed to trying to replace the sprag, as it seems like an easy job to do.

I also pulled off the left air filter to look inside. Do the injectors not prime the cylinders when turning the key to on? I did not try to start the bike with the filter off however.
 
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