dont get to frustrated w/ it. can you describe the noise you're hearing a little better? like is it constant through the whole powerband? only when cold/hot? you said the noise started after the cct install? did you mess w/ the timing at all or just rotate the crankshaft while it was still in time? was the tensioner out of the bike while you did this?

i cant imagine a f4i needing a new cam chain after 16k miles. and the tdc thing doesnt matter, especially if your installing the OEM hydraulic tensioner. even with a manual its not really necessary but i guess it cant hurt.