Check plug wires...

 

 

I agree with the plug wires. Had it happen.

 

 

Look at the both ends of each plug wire. Make sure that they are clean and making good contact. Inspect the insulation for signs of cracking. Check where the coil where the wires go into it.
While you're at it check the plugs.
You should also see if the bike threw any codes, since the CE light came on.

 

This may have nothing to do with your issue, but there was a time that my engine light came on intermittently, in much the same manner you described (2000 FXDX, so basically the same bike).

After my engine build everything seemed fine, until... I don't remember the exact sequence of events, but I was on a full day ride and my engine light started coming on here and there, at higher speeds. It would go out if I slowed down for a bit, IIRC. Shortly after, I detected an extremely annoying clicking sound from my cam chest. There's excruciating detail in this thread, but I'll cut to the chase so you don't need to read it:

https://www.hdforums.com/forum/dyna-...-sound-10.html

Basically, it turned out that my inner cam chain had developed a tight spot (or spots), possibly caused by a damaged tensioner. In short, it would bunch up ever so slightly at the point of greatest tension, then spring back to where it should be. I've named the phenomenon "Cam Apnea." Sort of like sleep apnea, except instead of your breathing stopping for a moment, the front cam would stop turning for a fraction of a moment, then spring forward to where it should be (I mean a REALLY brief interruption). Once I changed the cam chain, everything came back to normal and the light never reappeared. I'm not exactly sure of everything that can trigger that light on a carbed bike, but my theory was the Cam Position Sensor. I don't know why it didn't throw the light at lower speeds, but maybe the issue didn't fully present itself until engine speeds and/or temp was above a certain point...

Hopefully not your issue...

But here's my two cents with warning lights (TPMS on cars is a good example): When an annoying light comes on, we tend to look for all the reasons that may cause the light to come on without good cause... But sometimes the light is actually telling you something you should know, and is coming on exactly as intended.

Good luck!

 

if your check engine lite came on then back off u have a code stored in memory. check and see what it is

 

The ECU in our old twinks are pretty crude.

Knowing they had recurring issues causing their ommision soon after debut, I'd'd suspect the cam position sensor. Not sure if '01 had them or not, tho.