But the scanner will only check the computerized items.
Other items still have to be done the old way, good diagnostics.
If it is only running a coupleseconds before shutting down, It is not
likely something is getting hot and shutting you down.
Unless a main short shutting down the main circuit breaker under the seat in front
of the battery box.
You say only a couple seconds.
My guess it will be fuel related.
Pump, relay, filter, injector, regulator.
The ECM controls the relay. Normally the pump only runs approx 2 seconds at a time
while the engine is running.
Remember the old electric pumps we put on cars in the 60's and 70's?
First turned the key on and you heard it clatter for a few seconds?
It quit clattering when the carb float bowl was full and pressure was built up.
Pump would stop until more fuel was needed.
Pressure regulator works same way.
Now turn key on and you hear pump start (ECM and pump and relay are working).
You changed relay and did not fix it.
Your ECM is intermittent or a possibly faulty press reg.
Only way to tell for sure is a fuel pump pressure test.
Unless you have the right hook up looks like time for a dealer visit.
NOT recommended, but you can do this. Using a pair of hose clamp pliers (designed for pinching off hoses), You can clamp off the fuel return hose. Not completely just add some
restriction (this works like the regulator, but manually).
If it now keeps running longer, replace the regulator.
Then I would replace the hose too. They could be deteriorating internally.
This is assuming your bike is stock as you claim (no pciii etc).
This is just an idea of a starting point.

 

Thanks again for the info. I think I may see when I can get it in to the dealer to have it put on a scanner. If I have a day or 2 I will mess with it a little more. I know that I don't have a PCIII. The only thing I know that was done to the bike is an aftermarket set of mufflers and a high flow air cleaner. I keep thinking also that it is something fuel related too. Also when it dies I lose fuel pump and spark. So I'm getting a little bit moreinfo every time I messing with it. Thanks for everyones info.

 

check wires to fuel injectors ..remove and re-connect...
consider removal of gas tank per manual instructions... only 3 bolts after removal of seat...do not forget to empty gas first and look for any cut wires.
rule-out charging system per manual instructions. stator/regulator ok?
****rule out that the bike had a power commander or "other" removed and cable to ECM is loose or became loose..

 

'99 with only 5900 mile - I would be looking at a fuel problem more so then elect as gas will go bad over a period of time... Has it set any the engine warning lite yet??? I so you can have some one pull codes... But with a bike 8 yrs old and LOW mileage I would be looking at flushing the tank & replacing the fuel filter????

 

There was a recall on the bank angle sensor on early 2000 models. I'm not sure if this also included 99's as well. This sensor shuts off fuel and ignition if the bike is laid down. I'm not sure if the recall replaced the sensor or had something to do with the mounting like the recall that's out for my Buell Ulysses. On the Buell they are relocating the sensor because it can shut the engine down without warning. Might be an issue here. Hope this helps.

 

Thanks for everyones info. I had a low voltage code and changed the battery and fuel pump relay. When I changed the battery it cleared everything so I need to have the historical codes read and the only way to do that is to take her to the dealer. So I finally broke down and took her to the delaer to have the historical codes pulled. There are just sometimes that has to be done. I want it fixed I had enough of it sitting I need to get it running and get out riding.

 

Well be sure to give us feed back on what the dealer saw on the codes and the final fix.
Helps for future problems some one else is going to have

 

Thanks everyone for all the info. The ECM was not the problem. It was the Bank Angle Sensor. The dealer was Atlanta Harley Davidson they did what they said they would do and I have no issues with them. I would go back and recommend them for there Service Dept that is the only Dept at Atlanta Harley Davidson that I delt with.