the yellow vac lines with either red, green, or brown stripes have to do with the door locks. On the firewall, if you plug the three way connector and disconnect that little check valve thingy, you will cut the locks out of the system but not affect the shut off.
A little piece of a stick works great for this. I did the same thing because I am working on the floor where the lines run and needed to remove them, I also pulled the yellow and brown line out of the reservoir in the trunk, careful, cause there is a little grommet for that reservoir that is tenacious, and then suddenly will fly out and disappear as you try and pull the line out.
Its probably something really simple that would be worth fixing though, you have vacuum
, just too much! I second looking at the master vacuum switch