changed the cover and no oil change?
whats the compression check show?
it doesnt sound like anything happened to the bottom end.
run some marvel mystery oil for ~100 mi and change it & filter again.
if its not making any noise, in theory you should be OK.
NOW would be the time to do a proper build, if your going to.
remember: there is never enough time to do it right the first time...but always time to do it over.