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There are three hoses that connect to the air box. None of them are vacuum related.
The one towards the front of the bike goes to the air switching valve (ECU controlled) which then goes to the exhaust to burn off unburnt fuel especially during deceleration. This is what causes the pop pop when going down hill.
There is one hose in the middle which is a drain. I think it's clear to see if there is any water collected and plugged at the end. ( Why is the drain plugged? If it wasn't plugged it would be sucking unfiltered air through it so keep it plugged)
The third slightly larger hose at the back of the air box connects to the PCV valve which is your crank case breather.

Having any of these unplugged would not prevent the engine from starting.

The air box lid has a temperature sensor which you must have unplugged to open it. I have never tried starting with it unplugged and I assume that it would start with an error code rather than not start at all.

Happy to hear your V is running fine now, listen for any hissing sounds which could indicate a vacuum leak.
 

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2016 Versys 1000 CBF1000 VFR800
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Just throwing out there a feature of FI bikes... when you start it and don't let it warm up enough (it varies, but say off fast idle at minimum), and you shut it down, the ECU still thinks it's cold.. Next time you go to start it MAY be in enriched mode, essentially too much fuel...... hold wide open throttle while cranking and it should fire up in a couple of tries.... Needed air.
Of course it doesn't help if a vacuum line is off either, lol.
 
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