Ok try this. can you push the shaft into place with claw arm on & does it sit relaxed or try to resist. don't worry about circlip etc, it should stay there under no pressure. If no, why not, what's bent.

I guess the drum is retained as it should be under the little plastic cover above the drive sprocket. It's held over to the sprocket side so even if it was missing something it can only move towards the right side having the opposite effect with claw arm--so forget that just yet.

Usually happens hammering tight shift lever onto shaft splines or dropping bike on shifter side.  Real easy to do when changing shift shaft seal with clutch cover in place.

Shouldn't happen too easy if groove and clip are clean and in good shape... and if sharp edge of clip is "out".
 

Expanding pics up there's a lot of scratching going on--on the pin retaining plate but maybe just trying in the hope of hooking a gear.

RT325... now that you mention it, it could be the drum retainer missing.  shift drum could move over along with claw arm and then pull back over into place as drum rotates into next  gear? 

Easy enough to check.  Just pull little three bolt cover off on shift lever side and make sure retainer is on end of shift drum.

Yeas true, I ruled that out thinking if it moved over it would only fit tighter, but yes when it pulls back it could climb off if it had popped the circlip off the change shaft. I could just see the start of the three screw cover in place in the pic so ruled it out. But we don't know what's under that cover haha. Be unlikely but gotta be a reason.

I installed the new cir-clip on the shaft tonight and the dog leg stays on the pins as it should........

The claw arm falls naturally into place without any resistance

I am able to shift in and out of first gear with relative ease, but I discovered that I am missing a dowel pin.

Is there anything special to replacing these pins is it simply removing the phillips head screw from the side plate and installing the pins?

Also, What is unique about the "special pin" (part #10)

OK, not feeling very smart about this all.......  I went back to study it ad realized that I am not missing a pin......it is the special pin that is shorter than the rest!

I cannot shift into any gears other into into what I think if first then back to neutral.......   Should I be able to shift through all gears when the case is off etc?

Need to spin shafts to shift it so dogs and slots can align.

Remove the three screws that hold the shift drum cover and make sure the retainer and shim are there.

That's the plastic 3 screw cover above the sprocket. If unsure take a pic of whats in there.

Got everything back together....... started with on kick.......   Shifted through all of the gears just fine (So thank you for the help)

However, the clutch is slipping to the point were it only propels itself during idle.   I did not remove the rubber gaskets from the clutch plates as one person advised.......Could that be causing this much of an issue?

It didn't slip prior to me pulling things apart so I know that its something that I did.     Any suggestions on what to look at first?