Rough Running

I got 4 Codes

P0300
P0305
P0306
P063d

Dodge Ram 5500

Runs rough, i know the codes are cylinder misfires...

Pulled the fuel filter, there was no water in fuel light but the fuel filter has algae on the filter, so I do not know if some thing may be plugged.

Can I have some trouble shooting information on this, I hooked up an ethos scanner and didnt tell me crap.....