I've seen a few of these posts and none seem to be the same problem as what I'm having.

Bike cut out and died after startup, once restarted it ran fine and the idle was right at 1000. After about an hour ride on the highway with the throttle pretty wide open, it started cutting in and out. Almost as if it were shitting off and on every second or two. After making my way off the highway it completely died. It restarted perfectly fine. After getting it picked up and taken to the shop it wouldn't even stay running. The shop foreman took this issue on personally and could not duplicate the problem except for one time. He determined that the issue was due to an issue with my tune because it seemed as if the front cylinder was getting way too much fuel at random. He flashed the bike back to stock. After a full day of riding it didn't seem as if I had the problem any more but I didn't go too hard on it. The next day (it was raining) I had to get my bike home, and upon quickly opening the throttle it would slug out and cut off, I'm not sure if that's just due to the excessive water through the filter or the same issue again.

point is, anyone had this issue?
ive heard things about aftermarket fuel caps, and actually, the day after I installed my flush tank gas caps this problem occurred. Any ideas?

 

Is the bike stock? What model and motor? Which tuner and intake are you using?
It's doubtful that the motor can inhale enough rain to be a problem. And if somehow that much water got in there it would hydro lock.

If the new gas cap isn't vented properly you can have problems. What brand did you use?

 

Put the original gas cap back on and see if the problem goes away.

 

Also check your battery cable screws/bolts. Make sure they are tight.

 

 

 

Check battery terminal screws
check tune

 

 

 

Could be electrical .