Yes, vacuum line would effect things, but not as much as cranking RPM. Whatever RPM you crank at (mines around 210rpm) you need to set Cranking RPM about 100 higher than what you see. If its set too low, then the vehicle doesn't see the engine as cranking and doesn't apply startup enrichment, etc.
What software are you using.. Tunerstudio I hope? I'd recommend buying the registered version and doing a crank position sensor log from the Diagnostics tab (composite log and tooth log). That will ensure you're seeing a stable and correct crank signal.
Then ensure you're seeing spark with the tried and true "pull the plug and look for spark" method.
Report back, good luck!!