I'm just throwing this out there, but several years ago I had a similiar problem. Fuel pump went back. Replaced it. A few days/weeks later I started having the same problem.
It turned out that the return line for the fuel system was blocked and was causing an incredible vacuum on the fuel tank.
The pump had a hard time pulling against the vacuum causing all kinds of hard starting and hesitation. Eventually the vacuum was so bad that teh pump beat itself to death.
You might want to try loosening the gas cap. It will throw a code which will clear itself in a couple days, but you can see if some type of tank vacuum is the problem.