250-500cc Carb has me stumped..need help

I recently broke my fmf pipe and put my old stock pipe on and since doing that the bike wasnt running as well, i looked in the manual and it suggests a 40 pilot and 440 main for the temp/altitude i ride at.. and it had a 410 main and 35 pilot in it and i put in the 440 main and a 37.5 pilot and ran like shit with that main.. the throttle slide and needle and clip position are all standard as per the manual and the entire bike is stock as well and has got me stumped, i really only know basic carb tuning but i followed the manual and its way off and cant understand why lol

Opps forgot to mention its a wr360 and before i broke my pipe ran fine and seems to run fairly well now with the 410 main back in it with the 37.5 pilot but just cant see why the manual is so wrong and i cant tune it 100%

Word=Lectron
Check compression, reeds, reed block and manifold before chasing carb demons

Compression is fine is not long rebuilt and before i swapped pipes and had to try rejet it was also fine, rest of it is all fine also for the same reason it was fine before changing pipe and because id checked it recently anyhow.. but i think i found the problem but wont know for sure till i put the 440 main back in wnd try again, but bike was running bad yesterday and 20 mins into ride the needle clip fell off wnd main jet stopped working and i put it back together and ran fine rest of day (well as fine as was before i tryed jetting it to get it running 100%)