I'ed leave them out myself because stock didn't have them in there for a reason
on my 2012 Ninja the only Mod to the bike is a muffler and a fender eliminator
other than that she is totally stock.... however I think the previous owner added a jet kit to it and I may well take that out and go back to stock because it is running way too rich right now.
...the stock air cleaner works quite well but the stock muffler is a boat anchor and just needs to be replaced for something lighter and with better flow
....
all in all the little Ninja is a Marvel of engineering... she has plenty of power for this old man so I see no need to Hop it Up...
with the final drive gearing I put on it it cruises at 70+ MPH with no trouble
and is capable of tripple didgets on the spedo if conditions are right
that's plenty fast enough ! but to do that I had to install a 16T front sprocket on it. that changed the bike considerably I no longer had to shift 3 times before I reached 30 mph ....to me it feels like it was always meant to be
....
However the Ninja comes with some trade-offs..... it is by far one of the hardest bikes to work on I have ever owned. and I have owned over 70 in the past.... so many I have lost count !HAHAHA.
....
the problem with shimming the jet needle in my view is this.. as the slide goes up it lets in air and the needle jet lets in the fuel they are designed to let in a certain fuel/air ratio..... if you shim the jet needle you change that fuel/air ratio.... that is fine if it is running too lean to begin with but not so good if it is already burning just right.... you'll ruin the burn !
if the spark plugs look too lean then I would say yes to the shims
if they look to be on the lean side of perfect I would say leave it alone !
getting the jetting just right is a tricky business.... some call it Voodoo ! because it's a mixture of skill and luck and providence ! and a whole lot of patience !..... that makes it hard enough on any bike but on the Ninja that is so hard to work on.... well you get the picture....
..... that's my 2 cents !
good luck
Bob.....