Random engine misfire on cylinders 1, 2, 3 and 4

Okay, so I bought the truck listed above with a 5.4 Triton. It had been sitting for a while, so the truck used to I get up 45-60 MPH on highway and whenever I got to or right before the truck had a very hard time going and if and when I kind of put my foot into it RPMs go up, but the truck would hardly go anywhere. At this point is where I'd hear (under my hood) like a muffled backfire every time I'd hit the gas and it would go above 3,000 RPMs, but just would not go at all and the noise seemed to me to becoming from and also, I have a cracked air box where my air filter goes into to. I can only imagine that's part of the problem and when I bought the truck it was missing the strap that goes around the air filter box and recently, I have random misfires on cylinders 1, 2, 3, and 4, but I just changed out all of my spark plugs and all of the coils. And that is what's popping up on my code reader as 1st and 2nd most important fixes on the truck, and recently, my battery drained on the truck and charged it and started it but my windows don't work, back window, and power sliding glass doesn't work. On my aftermarket stereo my power wire from the back of the stereo is burnt. Please help. I've been dealing with this for 6 months now and simply need help. Please and thank you in advance.