This is a complex matter that is hard to pinpoint to just one 'issue.'
Currently, the AF 350Z has the XERD equal-length long-tube headers (which eliminate the cats completely) and Borla true dual exhaust. Both of these systems allow significantly greater amount of exhaust to flow through out of the engine. Many people believe that backpressure is necessary for good torque numbers (and therefore HP) on naturally aspirated vehicles. In other words, you want the exhaust gasses to be a bit pressurized in the piping. With the current setup, there may be too little backpressure due to the increased diameter of the pipes as well as the elimination of the catalytic converters (which, as you may imagine, act as a significant bottleneck for the exhaust to flow through).
Another possible factor affecting the situation is the stock ECU's overcompensation for the increased air-flow it is seeing via MAF.
The AF 350Z was one of the pre-orders with the first generation Z33 ECU. Currently, Nissan is on either 3rd of 4th generation of this ECU which I understand has many previous bugs resolved as well as some parameters changed to make it more tuning-friendly.
Of course, neither of these is an issue for the AF 350Z as we are going FI with a supercharger from our new sponsor - Vortech. Furthermore, this car will have a standalone management system of some sort in place to allow maximum tunability.
For your situation, as you are planning to remain N/A, I can make the following recommendations with confidence:
Intake: JWT Popcharger (cheapest, sounds great, and actually appears to add HP, which is rare for an aftermarket intake to do on the 350Z)
Headers: If you are in California, XERD headers are out of the question as they will not pass emissions. Otherwise, I strongly recommend them with the exhaust that I will mention below. Many 350Z owners have bought headers and then went to replace the cats with either high-flow cats or test pipes, which in my opinion is not a very smart financial decision, considering you can simply get the XERD headers and kill many birds with one stone - they are equal length, great design, and eliminate the cats so you don't have to make an extra purchase of high-flow cats or test pipes, which run well over $300 on their own.
Exhaust: After doing some research into what some of the Japanese tuners are doing in the exhaust arena, I have found that many are seeing great gains with a single exhaust pipe - the headers go into a Y-pipe, and then the single pipe is split up at the very end for the dual-exhaust (this is simply for the aesthetic value).
Invidia exhaust is a great pick - very reputable company and affordable price. If you want to go all out for an exotic exhaust, go with Amuse's Titan R1 - it weights a mere 8.7kg and Amuse claims 11whp gain on a dyno on a stock Z.
You may also want to contact a Nissan dealership and see if they will reflash your ECU to the newest version that is currently available. Some may refuse to do it, while others may charge a little, or you may get lucky and get it done for free. This is probably the most cost-efficient 'modification' available for the Z right now.
Again, I want to emphasize that Borla's TD exhaust and XERD headers are top notch in my view, and they should be perfect for 350Zs that have forced induction.
phew... quick question eh?