So did a handlebar swap 2 days ago running the wires internally. Bikes been running fine since i found an earlier disconnected alarm antenna connection. But today was on the freeway and bike started hiccuping, then when I exited the freeway bike stalled as I came to a stop. Proceeded to drive home...stalling 2 more times. Now the bike will idle on jiffy stand in neutral, but as soon as i right the bike up...it stalls. Checked battery connections and they are fine. I noticed when i looked around the electrical box that the stock wiring harness that is no longer connected to the ECM but connected to the black connector of the PCV was resting against the engine. The big plastic stock wiring harness seemed a lil singed on the plastic outside from resting against the engine. You can see the wires inside of it and they look fine....but do you think maybe one of those wires is the issue? Are those wires even doing anything at this point since they are the stock wiring harness and I have the PCV now connected to the ECM? Maybe another issue?

 

I am having similar issues with a 07 SE Dyna, and from the sounds of things it is in your security system, it is arming and shutting down the bike...in essence it is doing what it is supposed to do, but it aint doin it at the right time....and I dont know what to do about it as I am here searching for a cure for it myself.

 

Best way to make sure it isn't the key fob is to change the battey.that battery should last awhile mind you. Mine are going on two years.
Your pcV connector...of course it is still doing something,you have only by-passed the ecm signal through your pcV,so it has taken over. If you found it nudged up against the cylinder head I would pull that connection apart asap and look inside. check for melted stuff or even water can cause that problem. My first pcV install I left the connector zip-tied to the back of the fuse panel,black connector side down,and the first time I washed it it shorted out. I now have it zipped under the frame well away from the engine with the black connector up so it's now impossible for water to crawl in there and pool on me.
Also I placed two zip-ties on the connector itself so it cannot vibrate apart. You have two lights on the pcV one is power and should be green when the ign.is on.the other I think says check and should flash red twice and go off. If that red light is giving intermittent red flashes you have a connect.problem,and my bet is it is between that pcV black connect and the stock gray one gray

 

check to see if you have any diagnostic codes set.

Use this procedure:
https://www.hdforums.com/forum/3988078-post4.html