Engine Noise

Hi,
I got a 2004 Dodge Dakota with a 3.7L V6 engine. It has two engine problems.
1) It is ticking. The oil is fresh and of proper level. I changed the spark plugs. Next I checked all of the plug boots and all are operational which I have tested with a multimeter. In doing so however I have noticed that one of the cylinders (middle one on passenger side) is not operating. I have checked compression and it is good = 10kg in each cylinder. Also I have tested alI of the injectors manually and they all spray fine. Next I tried swapping the boots around and they all work on other cylinders but that one. The reason I think that cylinder is not working is because when I unplug any other boot's electrical connector there is a noticable change in the engine's idle. You can feel it strain. But when I unplug that cylinder nothing happens. What would you recommend I do next to diagnose the problem properly? Should I remove the valve cover and visually inspect what's going on there?
2) This is a more disconcerning problem then the first. It is making an awful bang sound every 10 seconds or so. It sounds like metal hitting metal. The sound is coming from somewhere in the duct running down after the throttle body at the top of the engine. When rpms are increased with an accelerator the bang becomes more frequent and gets a lot louder. Also, my new plugs are now all coated with black soot except for maybe two of them on the driver's side. Next, the check engine light is lit and it is giving 2 codes : P0128 and P0137 both of which are for downstream oxygen sensors in bank 1 and bank 2 respectively. And there is a foul smell coming from exhaust at increased rpms.

SO. My diagnosis so far is: Middle cylinder on the passenger side is misfiring/not operating thus not burning all of the fuel properly and dumping it raw into the exhaust system which has now been quite contaminated and thus spitting out check engine codes. My questions are:
1) WHAT is causing the misfiring/malfunction in the middle cylinder? How to diagnose the exact part(s) to be replaced?
2) WHAT is causing the nasty bang noise? Is it somehow related to exhaust gases backfiring from the middle cylinder misfire? Is the catalytic converter shot as well or just the senosrs? Why shows no codes for the upstream sensors? Wouldn't they have been contaminated by now as well?
I would sincerely appreciate some help/guidance as I am quite perplexed on how to proceed now.
Thank you,
Marian