The creaking could be certain pinch points where the top meets the CF covering of the rollbar in the back. Double check your clearance there. I was the 1st one who started this glasstop experiment and had to customize mine to make it fit. i.e.: sanding the rear of the glass top where it really connected / overlapped the rollbar CF and I also had to extend the original door seals of the top, the were 1/8" - 1/4" too short towards the rear which allowed water to drip inside the Roadster when it rained. I cut the seal and expanded it using styrofoam and some really good heavy duty black gasket maker, like the silicon stuff but thicker and stronger. Worked well and no leaks, I keep my Roadster outside all year since I don't have a garage.
As for the smell, I didn't have that. My top was sitting for some time @ MR.Fiat. Either mine didn't have the smell or it had time to offgas.
I don't use my stock Roadster top anymore, I put it on every once in a while for a change of look and lines. Makes the car look longer. But I typically roll in the summer with the soft top since I can just pop it off and toss it in the trunk, no top which is preferred, mesh top if its really sunny or a slight chill and I still want the sun/wind environment, and once temps start dipping down in the fall I throw the clear top on. The Roadster is small in the cockpit so putting on the stock hard-top or soft top really limits my visibility and cuts me off from the outside environment which the Roadster connects me more with each day and its always a pleasure capturing the moon at night above me while on a drive.