’01 silverado engine surging

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I have a '01 silverado 2500hd 6.0 V8 with 110,000 miles. I have been haveing a problem with power lose. The check engine light came on and I took it in to check the code and it said that there was a miss fire in 3 of the cylinders but it did'nt say exactly what the problem was. I changed the plugs on it and I still have the same problem. The symtoms are when I put the pedle to the floor I get surging in power like the engine wants to go faster, but once I let off it runs fine but it still doesn't seem to have all the power it should. The surging that it does isn't irregular either I could probably set my watch to it. Also when I floor it and the surging starts sometimes the check engine light will flash for about 30 seconds a then shut off. I did just have the fuel pump replaced, could there be any chance that its bad or could it be a O2 sensor, or maybe something else. If any one has any suggestions let me know. Thanks