I had something similar but from 2nd to 3rd for almost 2 yrs of ownership. I changed to honda mtf and no change. Then i bought a weighted shift knob and that finally solved the problem

 

I get the click sound too, when enigne is cold, also sometimes start from a stop, its totally normal to me.

Weight knob really helps!!! even on 2nd gear grinding, my 1st to 2nd sometimes grinds with the CR knob(which is light), but when i put on any weighted knob(1pound+-) it seems to happen much less.

or maybe do the DIY shifting shaft re lub... i havnt try yet but it seems gonna make it better.

really... our S is meant to be driving at high RPM......

 

I have the clunk noise also and the dealer states that is normal.

 

It happens to me from 1st to 2nd also.