Have you given the carbies a general clean as well, some of the poor idling coughing etc, can be quite easily caused by some blocked jets, or sediment being stirred up via fuel tank, float bowls etc..
You need - clean fuel, clean fuel lines, clean filter (if one is installed), clean carbies, ... then start making a few adjustments,
slowly slowly catchy monkey.
what model carburretors are on the bike?
what are the idle jet size

?
have you done anything else apart from adjusting needle clip position ??
what condition were the float bowls??? lots of sediment/varnish???
nearly everyone on this site has been there (some many times) done that ,, it gets better ,,,