The issue is with the Brotherhood of Steel Elder Namura(or whatever his name is). After finishing the mission where I have to kill/drive-off the NCR trooper in the nearby bunker I return to the Brotherhood bunker and go down the steps to find the elder standing there waiting for me to give my report. I come back later to find that on his way to the control room he is clipped on the MK turrets. After 10-15 minutes of pushing him to the door that connects level 1 and level 2 I had to punch him once and quickly run through the door with my fists still out to get him to follow me through then I feign hostility to get him to lay down arms.

After I push him all the way to his chair in the control room I try talking to him again but he still says to speak to him once he get's settled in the control room. Is there any console commands I could put in to restart the path he walks or make him reset at the door that leads from L1 to L2? Also, if I do put in such a command, does opening the console still disable achievements?

Thanks.

EDIT: I not using mods of any kind.

You would be better off just reloading a save game
If you haven't got one, try to figure out the script point and trigger it via the console. Check out the fnv wiki for that.