Agent M79 said:
Did they replace just the left side cylinder head with 3R2Z-6049-GA or both? Did they replace it with the alternate part number under warranty?
They only replaced the driver's side head, which coincided with the TSB on the Cobra. According to the parts database at my dealer, both the Cobra S/C and the Marauder share the same heads. The factory wanted to replace the head with the same part number, my dealer fought to get the new part number. 14.56 seconds later, I have a fully functional FrankenRauder

(my new nickname for it).
Yes it was replaced under warranty.
About your ticking... don't be paranoid, there is a normal ticking involved with injectors because of their normal operation (small pintles shooting forth and retracting very quickly, many times a second in some cases). Also, Sarge pointed out to me an interesting source of similar noise which is the pulsating of the fuel rails as the injectors fire... I'd never heard that one but it surely makes sense.
In my case, it was very audible with the hood closed from several feet away from the vehicle (if you can hear it from behind the car, you know you've got issues). With the hood open, the ticking can definitely be localized under the driver's side valvecover at about the second to last cylinder on that side, counting from the front (or if you prefer, the second cylinder counting from the firewall). We heard it in another MM's engine bay at Hershey, it's unmistakable.
I should have taped the sound before the repair, for reference.