First of all, it is alarming that you had to change the fuel pump, regulator, and secondary pump on a three-year old bike with less than a thousand miles. I had to do all of them, but over a period of five years on a 2008 bike that has more than 20k miles and has been used hard.
To the specific problem, it could be a crankshaft or piston issue, but it's difficult to imagine how this could have happened to a bike with just 800 miles. If it were me I would start by the least invasive tests and go from there, i.e. do a compression test first, if below specs then check valve clearance, etc.