I have watched the Dave Seeger vids and feeling good about getting this ct rolling. Bad bearings in one, another engine in shop with good mains. I can’t get the shift adjustment on the shift shaft to center on the tangs on pins on shift drum. The replacement engine has a pretty knarley shaft with splines twisted and bent a little at the very end. Putting the shaft from the bad motor in the good one and turning the adjustment screw the adjustment won’t get me centered on the tangs. Hangs out on the furtherest tang. I can round up another eccentric off another motor, could this one be worn too much. The shop good main motor was missing a lot of stuff and using the eccentric from the bad main motor and shift shaft from same. Is there another adjustment somewhere?
 

I'll leave this now i've typed it but shows how damn stupid i get explaining in riddles at times. So don't dwell on it haha.

I think you would need to be in third or even 4th gear not second or first, to get a true indication as neutral half movement gets in the way But there's only one accentric adjustment screw. Be careful going around as can wind it out. Screw it right in or as near as you can so you have a half turn of adjustment. Or in other words you get a 1/4 turn left & 1/4 turn right. Might get a small difference if you started with screw down rather than up & might be fractionally different from down coming up to halfway as opposed to starting at top & coming over to halfway. But difference would only be if you had to stop it short of halfway so incremental movements.

Now the short version. Only one wobbly adjusting screw, so need a bit more info if ya can't get it right. Or a pic of what's going on if possible. Twisted spline the gear lever end won't change things but if its had a good hit maybe something is more bent in the arm than the screw can overcome--guessing.

Do you have the goofy "mousetrap" return spring installed correctly? 

It always takes me a few tries.

Mark I have two shift shafts and the spring that encompasses the eccentric screw is installed the same on both. I didn’t remove them. RT the tangs on the adjuster do move back and forth they just max out at the forward tang pin and moving back to center won’t get far enough to center or close enough to the rear pin to center. I’m wondering if I have an internal problem. Can bent shifter forks cause this or another internal problem? I hate to reseal it and install it and have a shift issue. I am orienting it on 2 pins. 

So you have an arm with a BIg roler wheel held by a spring & sits into the pins holding it in gear?. The spring MarkT talks is on the gear change arm & the spring ears mut be untangled to point straight ahead as they sit over the wobbly adjuster?. If the springs have been off the arm they'll cross their legs. So assunming that's all ok--i'm stuffed. Idealy should be able to sit it in third-- then the wobbly thing should easily centralise the claw arm over the pins. So that's not happening?. Won't be an internal issue because even if you had no gears or shafts in there & just the drum & arm with big roller wheel it would still adjust to centralise. [in my opinion]. So i temporarily give up. Hate not getting to the cause. Cheers.

try to load a pic link if ya can.

Just had a thought. There's one short pin to do with neutral in a roundabout way although neutral is held by the ball & spring detent the other end--but. Could that short pin be in the wrong hole so your claw arm would never centralise oneway like that but hook it up a gear & it would show to be centralised. Alternatively & if all pins are untouched, are you trying to centralise in neutral--hook it up to third or 4th & check it.
www.partzilla.com/catalog/yamaha/motorcy...3/ct3/shift-cam-fork

Tonight showing my brother if I push on the arm it will come closer to center. Maybe I’m overthinking it but why do I have to apply pressure for it to center. I realize the shifting will do that in real world. There is no other spring to pull it forward. The stopper lever assembly and its spring doesn’t play into this. I’ll use my finger and tension the shift shaft and adjust . Seems the tension spring on the shift shaft 90506-09009-00 only pulls it down on the pins. I pulled another engine today but it’s got white death in the magneto. Guess I’ll assemble and see what happens with my best adjustment. I have a new stopper lever assembly coming with my other stuff.

The mousetrap spring on the eccentric adjustment pin... if installed correctly... should center the "claw"... that's why when you turn the eccentric it moves the claw back and forth so you can center it on the drum pins.

But I might not be understanding... a link to a vid uploaded to vimeo or youtube or a link to a picture on imgur or someplace would be helpful.