Need some help Running very rough

OK, I Have a 1999 Chevy C/K1500 one day it started running really rough, it was missing and doing a littile back firing. I replaced the cap rotor plugs and wires. But it was not sounding right, it sounds like something in the exhaust is plugged. I cut the muffler off and installed 2 aftermarket turbo mufflers. Also I hooked up one of the Snap-On computers (the Microscan) and it gave a code "P0300 Random/Multiple Cylinder Missfire" What else could be causing this, I am guessing maybe one of the cat's but if I go cutting anything else off this is going to get expensive. Any imput would be greatly appreciated.
Thanks
Billy

You might want to check the EGR valve.