You need to check your wiring harness from the voltage regulator out and make sure the mating connectors are clean. Use dielectric grease on the connectors.
Check your grounds up on the front forks. Make sure the battery ground is clean as well.
This almost sounds like you are having a bad connection since the regulator has been replaced. If the ground is not good, the regulator doesn't have a reference for the voltage. With a poor or floating reference (possibly to to a loose or dirty ground connection), the voltage will "float" to different levels and cause significant problems.
If the bike is a 2012 (read [email protected]
in your post), then it is under warranty so don't spend a lot of time on it. Let the dealer figure it out and fix it for you.
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2013 FLTRU, Jackpot 2/1/2 Stainless Ceramic Coated Head Pipes, Fuelmoto Stage 1 Intake, Power Vision, Jackpot Full Size Ceramic Crossover, MADSTAD 16" Windshield, Motolight Running Lights, Nostalgic Rails, Airhawk R, Hayden Primary Tensioner, V&H Roland Sands Slant Slip-Ons