I have been thru all this with my S4 and have cured all poor running problem by using a PC3 with termis and airbox mods then setting up and writing a series of custom maps , I now have a perfect tickover with easy running at low revs and great transitions to mid and onto the rev limiter , there are no glitches at all and around town the bike runs smooth as silk at 30mph in 4th gear .
I find that the TPS is most critical of all service jobs even if valves and balance are perfectly set the TPS is more critical for perfect smooth running .I check it now at 2 monthly intervals as it goes off very subtlely .