Does my 2006 GMC Envoy Denali 5.3 have fuel filter?

So, today we checked the rail as we were getting ready to drop the tank and there was some fuel pressure! We charged the battery and she started up! However she is running rough. Lots of knocking and hear some misfires. We barely got her over to autozone to get a diagnostic. Here are the codes it is throwing:

P0300 (twice)
P0016
P0101

Autozone reccomended cleaning the fuel injectors. Seems like there is too much going on for it to just be that.

2nd one seems to be crank shaft sensor, 3rd one is a mass air flow error (From what I saw) so im wondering if the knocking is a bad crank shaft sensor? Also, she was shifting rough. Large jerk and thump noise when changing gears.