I ended up doing a lot of side quests before going any further than novac, and have not entered the strip yet. I'm level 29 and put a lot of time into my character and cannot finish this quest without my save getting corrupted.
I clear out the basemant
Collect all the parts needed including the sugar bombs and turn them in then during the launch sequence I leave.
When I leave the basemant it corrupts every save file afterwords before I can actually launch the rockets. There was one change, when it first happened I had picked up the space suit and the save got corrupted when going from the basemant to the main building. I tried the basemant door to the main building and the outside to front door to the main building and they both corrupt my auto save and any other save the second I enter the main building. When I didn't pick up the space suit I was able to go from the basemant to the main building without it getting corrupted once but when I loaded the office I loaded my auto save and it got corrupted the second I entered the offices(ARGH soo close. So far the wikia has a couple of bugs noted that could be what the bug is:
From wikia Come Fly With Me page:
1. Picking up the Space suit in this quest CAN, but not always, corrupt save files.
2. (PC ONLY?) Entering the REPCONN basemant the 2nd time to talk to Jason after talking to him upstairs, or even simply re-entering any area of the the REPCONN building after "securing" the basemant might corrupt all subsequent saved files. A possible fix is to to use the "movetoqt" and "moveto ref id" console commands since the corruption seems to occur after using area transition doors within the building. (Confirmed unrelated to the recent patch)
3. The corrupt game save file bug may be related to faction scoring. Go away, do a quest that alters your reputation with another faction, and then re-try the mission.
4. Sometimes a save file from inside the room where you launch the rockets will become corrupt and crash the game if you try to load it.
Personal notes on 3 and 4.
3. I have a really high faction score with a lot of different factions. I'm not even hated by the powder gangers.
4. I didn't save inside the room, I make an auto save in the room with the makeshift beds before the entrance(sp) to the main building but only after I started noticing that my saves were being corrupted as a back up just in case.
I have no idea how to get past this and could use some help.