In lowering the top, make sure you have held down the lowering button until you hear a beep, that tells you that you can now pull down and lock the top in place. JFK 05 Roadster

 

I've had my roadster going on three weeks now.
I specifically remember what my salesman told me about how to bring the top up and ALWAYS turning the handle ALL THE WAY.
He also suggested bringing it down genlty (after the beep sound) by grasping the left side of the frame with the left hand......it does help to have two hands gently bringing it down and locking it into place.
I forgot to do it ONE time and I did hear that CLUNK. It's the metal hook slamming into the latch.
The reason why it's hard to bring down is because of the preset tension in the ragtop's frame.
It is good design I think.....it doesn't leak!! And that's a plus for me!

 

I also had the loud metal-on-metal thud when I pulled the top down. As PhillyXfire suggested, I also use my hand and slowly guided the top down with my hand and I now get a firm landing.

 

Try pushing up on the side over the driver door while pulling down. This makes it much easier. My wife does this to make it easier. It migh not be the right thing but I don't want the dealer to touch the top till I think they have had enough experience with these cars.

 

I, too, have found that holding up on the frame over the driver door while pulling the top down makes it easier to pull down and easier to control the clunk.