I noticed these two lines don't connect to anything... any input or link to a diagram would be great!

vacuum line by dtpaladino, on Flickr

vacuum line by dtpaladino, on Flickr
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Here's a pic of the stock set-up.
The VSV on your engine has been relocated too, with a direct connection to the air shutter bypassing the disconnected lines.
...
They are ... boost sensors to control the lights on the dash, one is for boost and the other over boost. They are fed from the crossover pipe
Some thoughts to consider.
The vacuum pot closes the shut off valve by having vacuum applied to it from the VSV valve when you turn the key off, the normal VSV is no power, vacuum passing thru to the pot. If the key is off and the motor dies the VSV is working (at least in this mode).
The rig has been off (no vacuum being generated) the vacuum pot and VSV has no source of vacuum except stored vacuum, when you turn the key it should shift the VSV to vent the vacuum stored in the pot and lines from the pot to the VSV, the vent allows the pot to open the shutter which allows the engine to run, either the VSV is not shifting or the vent is plugged. If the vent is plugged it will not allow the shutter to open, when you pull the hose off the pot you are making a vent.
The vent (since I don't know what rig you have) could have a filter (very small) pushed on the end of a nipple on the VSV or a rubber tube over to the intake hose between the air filter and the turbo (if you have one) or the intake tube.
If the VSV filter is plugged or the vent hose is pinched or plugged it will not allow your motor to run.
The VSV could also not be shifting. the power supply could not be making it to the VSV (the VSV shifts to run with power) if you have a broken wire or a bad ground the VSV will not shift to the run position (venting the pot).
I hope this helps.
Jim
no, and it's likely poached unless it's been wired with 12v.I have a 12V VSV, on a 24V truck.... is this normal?
appears to be two problems:The engine starts, runs rough for a few seconds and then stalls. When I manually hold open the shutter pot butterfly valve on the intake, it still will not run. Is my problem separate from the VSV?