Now Ive been slowly customizing & replacing parts on the bike for the past year, but I have yet to do any work with engine other than replacing oil & plugs.
kinda backwards....but ok.
you definitely need to complete the 3000mi recommended maintenance items.
this will alleviate the majority of the noises.
once you've done it all, and the problem persists, we can better assist.
the shop manual can be downloaded in the FAQ section of the forum, if you havent already done so....