Terrible running

Here is a video.

Another video with more detail.

Also, I cannot pull the sensor out all the way because the top bolt holding it in has stripped and will not move at all. So it will be a couple of days before I can extract it.

Never mind. I have gotten the sensor out. Here is a picture of it:

History on replacing the sensor. About a year ago I pulled the transmission to do the clutch but in the process of reinstalling it the sensor broke off the piece that holds it outside of the transmission. It fell inside hanging by its cord and since it was not made to go inside it in the first place it would not slide back out. So I had to make the transmission housing hole a little bigger the a grinding bit to make it big enough to pull back out. After that I replaced it with the current one in which when it was installed in the proper position the motor begins to run terrible. However, when it is moved into the odd angle it runs great and even runs great when I push on the pedal.

So I am pretty sure I solved the issue, though I do not know exactly how. But just in case someone else has a similar problem it is most likely not the crank sensor because I found that the vacuum lines were hooked all in the wrong places. So I fixed that and then the line that goes to the side of the valve cover had a crack in it. I replaced it and it ran and idled so much better though at first it was idling around 1,200 rpm and I could not figure out why. I checked lines, wires, sensors not even a peep from the check engine light, but when I pushed the clutch pedal down it went to about 2,300 rpm and that kind of scared me. So I let go and it went back down to a steady 800 rpm and when I push the clutch pedal down it does not affect the rpm at all anymore.