Switching from helium to nitrogen as a carrier on HS/GC-MS(5977MSD/8890 GC/PAL RSI 85)

Nitrogen cannot be used as a carrier gas into a GCMS.  Nitrogen can be used as vial pressurization gas in the HS.

The alternative to helium is hydrogen. Please follow all the recommendations here:  

Handle the Helium Shortage | Agilent

https://www.agilent.com/cs/library/usermanuals/public/user-guide-coverting-ei-gcms-instruments-5994-2312en-agilent.pdf

Shimadzu has been playing around with nitrogen for EPA 8270. Is the issue turbo or rough pump related?

It is neither turbo nor rough pump related. The available helium conservation module that mounts into the GC switches to nitrogen and the system tolerates pumping that just fine. Nitrogen is tough in any GCMS ion source due to chemistry and physics. It is a much larger molecule than either helium or hydrogen and gets in the way. It also ionizes and can cause unwanted space charge effects and odd spectral tilt.   

In the GC column, the optimum linear velocity is about 1/2 of that for helium and ~1/4 that for hydrogen.  It is necessary to run at lower flow rates for decent chromatography. https://www.chem.agilent.com/cag/CABU/carriergas.htm .