Removal & installation of the intake manifold is @ 3 hours, depending on the tools that you have and familiarity with the components. The bolts at the back may be problematic and the cooling line may be damaged if you are not careful. I suggest you tackle the transmission problem first before doing the plenum.
The shifting issue may be due to the condition and level of the ATF, dirty filter, failing sensor (VSS. TPS, etc), control unit (TCM) or the transmission itself. Better have a free scan from Autozone and the likes as there could be 'ghost codes' related to transmission problem.
How's the color and level of the ATF? When the ATF was replaced, was it a FLUSH or just drain and refill? Have you ever inspected the ATF filter?
Refer to the AT (Automatic Transmission) chapter from the FSM (00 Maxima as I'm having problem opening the 01 Maxima AT chapter). Look for pages AT-60 for Diagnostic info; AT-90 for Basic Inspection and AT-102 for Symptoms Chart. There are lots of useful info from this AT chapter.
http://www.nicoclub.com/FSM/maxima/2000/at.pdf