Motorcycle randomly loses power and shuts down?

Just bought a 2013 honda shadow 750 from private seller, only 3500 miles on bike. However when riding bike for some reason loses engine, feels like one of the cylinders stops firing
Engine light goes on and motorcycle is unable to gain power, if i pull i wait and pull in the clutch it restarts and then can ride again for a bit before doing it again. At a certain point however the bike would even turn off, but would start back up again no problems.
i say it feels like one cylinder stops firing is because engine sound changes, bike is unable to climb revs / pull bike. However still running. This is fixed by either turning engine kill switch on / off and turning bike on again.
bike has 2 spark plugs per cylinder and though it could be bad spark plug but sometimes it will run for 15+ miles without giving me problem and then in a course of 1 mile i won't be able to get past 30mph ( ON THE HIGHWAY )
Bike has a non stock air intake, exhaust, and power commander.
Any more info needed ask away, if anyone had idea where to start looking for the issue?

Put the stock intake, exhaust back on and see of that helps. Make sure all seals/gaskets are good/immaculate, even a pinhole in the intake can screw everything up.

Millions of dollars went into developing a balanced system/engine from intake to exhaust with very precise fuel/air mapping. Tossing on random aftermarket bits can throw it out of whack.

I'd start there.

From there, I'd need a shop manual and a lot of time.

Check plug caps, coil and wires going to ign coil

A data logging multimeter is a wonderful tool for troubleshooting intermittent electrical problems.