Starting/knocking

[7.3'00]

Just recently my truck has been having a few problems.
First-occasionally ill try to start it up and the truck will go up to 600rpms fall back down to 400 waver back up to 600 then die. I will turn the key off and try again and same results. If I put it in nuetral and try and start it it will fire right up and have no issues.
Second-Ever since this has been happening when I am coming to a stop I hear a slight knocking, seems to be on the left side?

As of right now the truck is stock aside from 6637 filter & straight pipe. The knocking kinda sounds like it may be coming from air filter, but I could be wrong. My chip is in for a reburn so there's no chip on it.
I put an old Hypertech power programmer 3 on it but I don't think it did anything because before when I had it on there it would black smoke a small bit but I took it off to put my chip on. I put the programmer back on while my chip is in for a reburn but I don't thinks it's working. It won't even turn on now when I try to plug it. Also I know that I REALLY need a new air filter because mine is very dirty. I have one in the way now, but could this be causing this? I wouldn't think so because it will start if it's in nuetral but just a thought.
Any thoughts or advice appreciated,
Thanks Austin