250-500cc Wr300 6speed

we have all the parts in my 2011 wr300 to convert to a 6 speed, however i can only get it into 1st neutral and second...
Any suggestions

Have you assembled the motor? I always put the transmission together in the clutch side case and then made sure it shifted through the gears by spinning the clutch shaft and working the shift drum by hand. If it won't shift then without binding or raising one of the shafts then you have an issue and need to check your assembly. Then I actually put the cases together without the crank and make sure it shifted with the shifter mechanism. I had an issue with the shifter mechanism the first time I did it and had to make some change. Unfortunately it has been so many years my CRS doesn't allow me to remember details. It can also be a shimming issue. You always want to keep the shims from the factory cases with those cases. These are the shims on the outsides of the driven(counter shaft) shaft. The older cases tended to be looser tolerances than the newer cases so if you just use the shims that come with the doner tranny it is often too tight. This can affect shifting. I wish I wasn't getting so far removed from the conversion as it is a foggy memory at this point in my mental aging.

yes we did all that and it shifted fine until the shift shaft is installed and shifted with the shift lever

You are using the donor tranny shift shaft and shifting parts? I wish I could remember what issue I had before I got it working as it sounds like what I found. I know that you have to use all the shift shaft parts and detents from the donor tranny. I think what was happening is that when I initially assembled the shifting parts weren't resetting to allow another shift further than going from 1st to second and back. I am going to see if I can find my pictures from the install. It will be on an old album that is buried under 12 years of other stuff so give me a bit of time. I think I had something in backwards or was missing a return spring or the original fork that works the shift drum was bad.
Sorry you are dealing with an old man here.

Stick with it though as the 6 speed is so much better.

yes i will stick with it! this "old" husky is the best bike ive ever owned!!!