Ive had a few 300zxs
From what your saying it's possible eithe vacuum line is off
Or
The fact you have 2 inlet manifolds doesn't mean you can run 2 induction cones !
The 2 inlets actually share the one MAF sensor located under the centre panel between the head lamps
This could very well be the problem if both inlets air getting different air pressure ...
I'm not sure if your turbo or non turbo but I'm sure it applies to either set up
Gathering what your saying I'm assuming it's non turbo as this wouldn't be possible to run this setup you have with an inter cooler ...
Reverse engineer what you have done I'm sure there is 2 vacuum lines which you have prob left off
If its not that
Put the original piping back on and check that if you disconnect the piping on the passengers side
Do you start getting the same problem
I'm sure it's down to different pressures in the inlet or vacuum hoses