From anyone's experience, is 140 secondary mains too large? I had seen some posts that 40/70/140 was a decent setup for pods and exhaust.
I've run 35/70/140 with K&N pods and a MAC 4->1 exhaust on my 1980 750E1 for several years without any problems . I now have an airbox and Delkevic and I think the Delkevic if anything may be a smidgen more free flowing than the MAC so your jetting should be fine and certainly not to large.
Download a copy of the manual here. Click the Articles tab, Service Manuals and select the GPZ750 Base manual. At approx page 150 there is and excellent description of how the carbs operate. At 3/4 throttle and up, everything is running on the main jets (needle, primary and secondary) and also dependant on proper operation of the diaphragm and air jets. You may need to inspect and clean if necessary.
You say "not bogging" so maybe electrical? low battery voltage ? low voltage at coils? poor electrical connections ?
Check voltage at the coils with ignition on and bike not running.
PS where did you purchase the #40 pilots ? Was it these ones from Jetsrus
www.jetsrus.com/a_jets_by_carburetor_typ..._keihin_3M_slow.html
No problem with these. ...... except maybe the $. Just wondering if there may be another source.