This is what the punch mark should look like.  The slot in the lever should line up with the punch mark.  If yours doesn't have a punch mark, try to orient the lever exactly as shown in this picture.

When it's out of whack, the shift rod hits the alternator cover on the upshifts.  Like this.  Note that the rod is also bent.

Youa also must be concerned about clearance between the shifter lever and the footpeg/frame.  It gets close on the upshifts.  If the lever on the transmission shift shaft is out of phase, or the rod is too long, the shifter lever will hit the footpeg/frame before the shift is complete.  Again, only on upshifts.

Whoa! Great pictures thank you a ton bro!

Just got the rod in the mail, I should have it on tomorrow after work after I change the oil.

I'll upload some pictures of the bend also.

Appreciated!

Justin good point about why it got that way, definitely a lot to consider here... I'll be keeping a spare in my backpack just in case.

So.

Turns out I'm dumb as hell.

The Rod is not bent -- I think at this point the shifting issue has been poor shifting on my part.

BUT - the previous owner put higher risers and handlebars on the bike -- the clutch cable is routed between the triple tree and the tank, (I'm guessing they did this cause of clearance on the new risers/bars). I think because of this the cable is not adjusted properly -- also when resting on the stand, the cable is being pinched between the tank and the tree -- the rubber on the cable is worn down so much that the wire is exposed/eaten away at.

I think replacing the cable is one option, but i've been thinking about upgrading to either Murray's or Vers's Carb kit -- and I think they include a new cable with the kit. Is this line generic and could it be replaced with something longer?

Edit: Got my cables mixed up -- anyone know where I can get a longer clutch cable?

Thanks