2002 TRX250EX transmission/clutch/gear linkage issue

I purchased a 2002 trx250ex that was overheated and blew the centrifugal clutch. Using the service manual I repaired the centrifugal with a new one way bearing and the entire new centrifugal clutch. I replaced the crank as the bearing in the connecting rod gave out. I have replaced the top end as well. My issue that did not happen until I replaced the crank and rebuilt the transmission is the quad engages in reverse while in neutral with the neutral light on. The quad works properly in reverse as well and will cycle through the the forward gears. At first I thought it was a clutch issue but now I am not sure. The one way bearing in the centrifugal allows the clutch to move freely if I rotat the drive shaft forward while in neutral but it catches and forces the reverse engagement while spinning it in reverse. I feel like there should be an idle gear in the transmission that allows the engine to rotate the main shaft while allowing the countershaft to spin freely while in neutral. The only confusing part of the installation for me is the picture showing the neutral switch rotator on page 12-16. When I install the shift linkage on page 10-5 and align the dowel pin with the boss it changes the position of the neutral switch rotator to the 2 o clock position instead of 4 o clock. Any help would be much appreciated.