Motor makes clank sound. Help please

[Tlotusa]

I have a 5.7 mercruiser on a 1996 bayliner rendezvous 26'. I just bought the boat and on my first outing hit a huge rock just out of the dock on the maiden voyage. Boat sat a couple years so I was running bad gas with some new, so ran rough from the beginning. After hitting the rock returned to trailer and brought it home. Cleaned carb, changed plugs, cap, rotor, wires, changed oil, fuel water separators, lower unit oil. Cranked boat and it ran a lot better but has a random miss, well I'm calling it that, it makes a metalic dull thump that sounds deep in the motor. Sometimes it will go a few seconds without doing it and other times it seems like it's every revolution.its bad enough the whole engine wobbles a little when it happens. Does it at idle and in gear. In gear it's more noticeable. At no wake speed it will do it randomly ever 1,3,5 seconds or so totally random. It's almost like a transmission banging into and out of gear but it does it out of gear too. I don't know if it was like that before the trial run or if it started after I hit the big rock at 1/4 throttle and it killed the engine. Still gets on plane and at about 60% throttle the miss is less noticeable but still there. Is the motor toast? Please give me possibles