2006 Chevy Colorado Multiple Misfire

I had a misfiring problem and brought it to Autozone. They ran a diagnostics on it and said it was a number 1 misfire. I changed all the sparkplugs and the number 1 boot. It started running great and my gas mileage went up to where it should be. I drove it about 300 miles and it started running poorly again. I brought it back to Autozone and they ran another diagnostics on it and said it was a number 1 misfire again. I was told to switch the number 1 boot withthe number 3 boot to see if it changes from number 1 misfire to a number 3 misfire. If so it was a bad boot. I did that and brought it back to them for a third diagnostics check and now it is saying multiple random misfire. I was wondering what i can do to fix the problem myself. And maybe if it could be the box where all 4 wires run to. Please help. Thanks