So I have to kill the course at arcjet systems to complete this quest. This is like the third time Pam has given me this quest. This time however the course seems to be in an area I can not get to. I saw that you explore the place with a BoS person on a quest. I however already eliminated the BoS so now I can't get to the xourser. Anything I can do?

If this is on the PC, then you can use tcl to see if you are able to cheat to the appropriate area. movetoqt might be better. Arcjet is comprised of two different maps. One before you do the mission with the BoS where the entrance isn't almost completely destroyed and one where the Synth have attacked.

Forgot to mention that there is a bunker with an elevator to the Junk Jet area. The BoS mission powers up the elevator, but I am not sure if you can get to the area without doing the mission.