Dealers are notorious for not doing a good complete "Setup" of new bikes. This seems to be even more likely with Suzuki dealerships for some reason. The setup tech, usually the least experienced in the shop, should have not let the bike go out with vibes like you are indicating.If the dealer gives to any resistance, find another dealer, or go directly to Suzuki's headquarters for resolution.
I think a bad setup would only impact peripheral items like handle bars, cowling, exhaust, etc. I don't recall off the top of my head but the post-ship setup is mostly add fluids and attach, tighten and adjust a few items after taking it out of its crate. Its not complicated which is why the rookie gets the job and those steps are unlikely to cause the vibrations described by the OP. Based on the symptoms it isn't suspension/wheel out of balance/alignment but something with the motor.
I'm betting it's poor TB sync causing the issue, or could be bad engine balancing at factory, either way, make them fix it...
I agree and disagree with caveats.
OP is chasing his tail. The TPS and TB Sync would not cause engine vibrations at 5000RPM but would only cause idle and poor performance coming off idle. It is important to note that "TB Sync" is ambiguous and needs to be defined. For 2007 models and later the TB Sync that the service manual describes is adjusting the idle air screws only. This adjustment balances the air flow between cylinders at idle when the throttle (and thus throttle plates) are closed. It just makes the bike less lopey at idle and makes for a smoother transition from idle to open throttle. It has no effect on cylinder balance after throttle is cracked open even a little so cannot be the cause of vibrations at 5000RPM. As for the TPS, it has an adjustment range of about 5deg and, as far as I know, assuming the sensor is good if you put it at either extreme the bike would still run but would probably have bad off-idle, poor low/mid throttle response and perhaps poor gas mileage due to bad data going to the ECU. In any case, I don't think it could cause engine vibrations at 5000RPM.
For the pre-2007 models (in addition to the idle-air sync) there is a "TB Sync" procedure in the manual for adjusting the sync or balance of the throttle plates between cylinders by adjusting the linkage between the front/rear throttle body. The modern manual has no such procedure and says don't mess with the linkages as this is set at the factory, there is no field procedure to fix this and the service department can only replace the TB's if needed. If the throttle plates are imbalanced due to a bad factory set or someone adjusting the linkage screws this WILL cause vibrations at 5000RPM and across the whole range. This is because unbalanced throttle plates means one cylinder will be generating more power than the other. Because of this history, it has been suspected but not proven, that on occasion a mechanic has done a service on a newer bike but used his experience from the older models, i.e. he adjusted the linkage screws thus putting the motor out of balance. Suzuki needs to update their manuals and training and, most importantly stop calling the "idle air sync" a "throttle body sync" to avoid confusion.
Regarding the OPs problem, I think it is either a vacuum leak (which can put the cylinders out of balance) or imbalanced throttle bodies (from the factory or due to a mechanic's mistake). I would continue to press the issue with the dealership and at least get them to rule out a vacuum leak. If it is bad throttle bodies (which I think it is and discussed here in post #3
) then it is unlikely that the OP will get any relief from the dealership. They won't troubleshoot that and won't fix it, unfortunately you are on your own. As discussed in post #3, my new-to-me 2014 which I bought with only 3700 miles is way to viby and I suspect out of balance TBs. The previous owner had the dealership do all the service so I suspect a mechanic messed with the linkages. Also, the bike is a bit lopey at idle and the rear idle air screw is noticeably raised above the level of the throttle body which is another clue.