Engine judder the bike as been in storage, everythings been cleaned out or replaced ticking over lovely with a thump, thump thump. i put it on its stand and into gear as it runs its starts to judder,then runs a bit more, then more judder gradualy getting worse,if i put it into neutral and it ticks over fine. i love this bike so any help would be great.

SOURCE: gear/clutch problem

does not seem like the waterpump. is the clutch set too loose?
usually in wire based clutches, if the clutch cable is set to be too loose, or if it is frayed, and needs replacement, the bike will jump and stall.
check that.

SOURCE: Engine stalls when engage in any gear from neutral.

CHECK THE SIDE STAND SAFETY SWITCH IS OPERATING

SOURCE: I have a suzuki drz 125l 2004 model that currently

okay theres a couple possable things that can cause this .... carbon on the valves, ran hard,not frequent oil changes, low on oil, cheap oil, spark plugg is too long , too much oil somtimes causes this,crank case breather plugged,it all depends on the way it was treated in the past or the present
i change my oil about every 15-20 hours keeps debre down and less friction on engine,remember this is not water cooled! so use the best 10-40 oil or atleast good known oil and run some seafoam through the gas,it will take that carbon off . and if you dont have a inline fuel filter u should get one they really save carbs and there only $3.00 at oreily! hope this helps <walker>

SOURCE: The bike will not go into neutral gear when engine running

my husqvarna sm450r does exactly the same thing and my girlfriends yam virago is just as bad, i think some bikes are just too tight, rocking works or try finding neutral as you roll to a stop, on both our bikes it does the trick... nothing worse than trying to find neutral with your hand lol

Dude 48 bikes, impressive! im up to 9 in 20 months since my Ls :)

SOURCE: Suzuki GSF400 Bandit problems with tick over.

as you have replaced carbs you will need to retune for fuel intake also check its getting enough air ie.. air filter has been changed or is clogged