engine knock

well, i did a classic,i let the air cleaner nut vibrate off the post into the carb while the engine was running.shut engine off ,pulled plugs and used magnet to try and retrieve nut,no dice.pulled head and found that nut was aluminum and wound up in no. 3 cyl. looked like the only damage was minor scratches on top of piston.had a inspection and valve job done on the head and checked push rods, all looked good.put everything back together and engine had knock which sounded like a bad lifter to me,replaced lifters ,but knock is still there.i'm getting a little discouraged and would really appreciate any ideas that you guys could give me. the engine ia 2000 model 3.0 liter merc. thanks for listening to my tale of woe.
REB

you could have spun a bearing, if push rod was not bent, you said you put new lifters in did you set the lifters to specs unless hydraulic, how deep is the knock

allso check the plug for that cylinder to make sure end is not screwed up

the lifters are hydraulic and new plugs were installed,how would i check for a spun bearing?
reb