intake vacum on a diesel?

[1slowvw]

hey folks it seems i have run into problems once again, after having a mechanic do my last timming belt it failed so I was forced to do a motor swap....again. After dropping the new "good" motor in i found it to have a rough idle, and to stall out after a few minutes it will rea vacume on the boost guage when I tap the throttle, and it has a miss at higher RPM's; It does have some small shampaign sized air bubles in the lines but i have seen worse run decent. I am wondering if what this could be. Would incorrect timming cause this kind of behavior?
The coolant is clean no oil in it which leads me to think its not a headgasket, but feel free to disagree.

Thanks
1SlowVW

PS: I am currently running turbo to open air, I don't make a habit of it but I thought i would point out that a plugged filter is not the source of the vacume.

[jtanguay]

i would imagine that highly advanced valve timing could result in vacuum...  but your valves would be slapping (or other way around) the pistons by then.

how much vacuum are you registering?  and don't run the car too long without a filter... very very bad for turbos!

[1slowvw]

yeah I never run without a filter normaly, but I wanted to check to make sure i wasn't getting vacume from the intake system somehow.
As for how much vacum i would say around 2 or 3 inches or mercury(or whatever the mesurement is on the guage.

1SlowVW