I have sold hundreds of The Fidanza Flys and Exedy stock clutch kits without one single complaint.
If the fly is fitted as per the manufacturer's fiitting instructions then you will not experience any vibration.
What you may be experiencing is if you labour the car, say driving at 30mph in 5th or 6th gear then you will get a roughness through the car. This is a characteristic of the single mass fly because the inertia has now totally changed and there is no damping from the single mass fly.
A slight change in driving style will quickly resolve this issue.
The extra transmission noise that you are experiencing up to around 2000rpm is just the gearbox idler gear, again caused by lack of damping from the single mass fly and does not pose a premature wear problem.
Both these issues are characteristic of the single mass fly. This is a normal effect that is well worth the added performance.
The difficulty that you experienced with the shift between 5th and 6th would only have required the shift gate plate to be adjusted.
If you are experiencing a genuine vibration, which could be caused by a badly fitted flywheel and excessive flywheel run-out is evidence of an improper fit, then I would suggest that you take the car back to the garage that fitted the clutch and perhaps also make the people who sold you the kit aware of your issues.
Hope this helps.
Alex.