My 2¢,
First, replace those clutch springs with Barrett brand HD ones, the Ninjette, and EX both suffer from weak arse OEM springs. also you might want to look at the neutral position parts, there is a spring(part# 92144) that also is weak, and wears out, sometimes it need to be replaced, also part# 92043 wears as well.(see pictures below)
http://www.partzilla.com/parts/searc...%29/parts.html
Second and third, service the carburetors properly, contact @
ducatiman for your needs.
What kind of oil did you use? Also is it just shifting poorly, or is the clutch slipping??
And lastly, check your alignment, forks, etc.. have you ever serviced the calipers? I'm guessing not, add that to your things to do list as well.
Any questions please feel free to ask.