I purchased the S5 bike on 10/20/2013. By 12/5/13 I had a creaking or popping sound coming from my bottom bracket too. To make a long story short, my local bike shop changed out the Rotor bottom bracket bearings three times, the Cranks twice, Pedals once, COMPLETE FRAME REPLACEMENT once, Chain, Rear Cassette, Seat and finally after about 8 trips into the shop the mechanic said "if this was his bike I would change the Rotor cranks to Ultegra."
On 7/23/14 He changed the crank to the Shimano Ultegra 6750 175 34/50 and added the Shimano Hollowtech II Adapter (leaving the BBRight Bottom Bracket). This fixed my problem and I did not have any issues for over a year. On 9/19/2015 I was informed I needed a new BB as they will only last from 3 months to several years. I have an issue with this as I have a 2003 Trek 5200 carbon that has never had any BB issues with over 10k miles. Anyway the new BB Rotor BBRight Shimano bracket and bearing was selected to eliminate the adapter. I will cross my fingers that this works. I agree, I am sick of riding my bike once and dropping it off for a week for repairs. My bike shop has been great about the repairs and warranty replacements but I am sure they are sick of me and my bike! I have some out of pocket expenses, as well as no bike to ride when the S5 is in the shop. I would take a new 2015 S5 with the Dura Ace Di2 group in exchange for my bike problems if Cervélo is listening????
I'm in the process of moving to a shimano crank too, I have a click on the drive side under hard pedalling with my rotor 3d+ cranks, the problem goes away when I grease the axle and bearing race, also the amount of preload affects the intensity and occurrence of the sound. I noticed with my rotor crank that it slides in and out very easy, compared to my other shimano bikes which have a much snugger fit.
I believe the noise comes from the steel bearing race on the aluminium crank shaft. Aluminium is a softer metal too which doesn't help. I've ordered some wheels mfg adapters, I'll see it how it goes. I've noticed on my old threaded shimano bikes the bottom bracket has a delrin/rubber interface between the crank shaft and bearing race, much like the adapter will perform.
Will be interesting to see if the noise stays away with the proper bb cup, since you'll be going to a metal on metal interface with the bearing and shaft.