I had the same issue with my 3.0 TKS when it was new last summer. I have a Bayliner 175, and i was really surprised to hear such a loud--sounded like a valve tick--on the maiden voyage. Since the boat was under warranty, I took it back to the dealer and they serviced the engine. I had many responses ranging from you will need a new engine, to finally discovering it was the mechanical fuel pump ticking on the cam. Another concern was the large amount of metal shavings on the dip stick from the arm on the fuel pump wearing down. When you unplug the line from the fuel pump to the flame arrestor, the noise stopped or got much quieter. Also, the noise seemed to be louder when the engine was warm.
Mercury covered a new mechanical fuel pump, and denied they had any issues. Sure enough, 1 month later, the ticking started AGAIN! I took the fuel pump out, and the arm was showing lots of wear again. Since Mercury couldn't seem to fix my boat, I installed a Holley electric fuel pump, and problem SOLVED! Easy fix for around $200.00. After writing a letter to Mercury about my disappointment with my new engine and a request for my $200.00 repair for their faulty engineering, I was denied my claim. Needless to say, I will not be purchasing another Mercury product due to their poor customer service. It was very discouraging to buy a brand new boat with an engineering defect on the fuel pump that the manufacture simply didn't seem to acknowledge.
To everyone out there with a 3.0 TKS with the same issue (according to my dealer--it is a common issue that Mercury should recall), I would recommend an electric fuel pump install. It was very easy, and if you'd like pictures/instructions, please let me know!
It's just not worth damaging a new engine with metal shavings. I know it doesn't matter to Mercury, because by the time the engine shows damage, it will be out of warranty!!