2000 3.8 Cylinder 6 Misfire

Hi everyone. Right before Christmas, my 2000 Mustang's fuel pump went out. I swapped out the pump and filter and it fired right up. Ran great the rest of the winter. About a month or so ago, I noticed that it was cranking a couple extra cycles before firing up, usually with a cold engine, but sometimes (but not always) when warm. I pulled codes P1414, P0455, and P0306, cylinder six misfire. It was due for new plugs and wires, so I put those on today. When I started it up to idle for a minute in the garage, before test-driving it, it still cranked a couple extra seconds, but did start, and more alarming, I smelled a burning rubber smell after about 20 seconds. I shut it off, and I hooked up my scanner, and pulled the same three codes. I just got the scanner about two weeks ago, and am still learning how to use it. I cleared the codes and re-scanned, it showed no codes, although my CEL is still on. But the smell is what's concerning me the most. I made sure to keep the wires away from any hot parts. For the misfire, could it be the coil pack? I don't know what could cause the smell. Fortunately, I'm working from home and haven't needed to drive much, but I'm trying to learn how to do some of my own work. Thanks if you made it this far.

Edit: I forgot to add that when I took the cold air intake off to get at the passenger side plugs, I noticed that one of the hoses was off. I know I didn't take it off, but after I put the intake back in, I reconnected both hoses. Hopefully I did it right. There should be two. Sorry I'm not great with all the terms yet, I'm still learning to do all this solo. As encouraged as I was when I put the fuel pump in, I'm that discouraged right now...