Hello y'all, finishing up my first full motor rebuild ever on my AT1B 125cc and I ended up with some extra parts. 

Firstly there was an extra thrust bearing behind the clutch assembly which is visible in the Yamaha parts diagrams which shows two thrust bearings, while my service manual only shows one. And an extra ball bearing was with the clutch push rod I'm assuming to make up the difference of having an extra thrust bearing. When I installed bot thrust bearings, all the gears seamed to be about 1/8" out of alignment and seemed to line up perfectly when I took one out. There was also some rotational scraping on the inside of the clutch side crank case cover which I'm assuming is due to the extra thrush bearing too. Am I wrong to assume I should be installing with only one thrush bearing? 

Lastly, after reassembling almost everything I came across this rubber damper/stopper/plug? Maybe garbage from another project? I'd really like to know if I forgot to put this back somewhere, I've scoured the yamaha parts diagrams and haven't found anything that looks like this. Please tell me this doesn't go inside the crank case, lol.

 

Greetings from Tennessee!! Yes the ball bearing goes with the push rod there is only 1 thrush washer also if you bought a new seal kit that’s probably where the plug came from 

Not enough detailed info on what you mean by an extra "thrust bearing".    There is a thrust washer plus a bearing assembly which consists of a flat roller bearing and a thin thrust washer.  The parts diagram does not show the thin thrust washer that is part of the flat roller bearing. 

If you had two complete flat roller bearing assemblies I'm pretty sure the spacer the outer hub rides on would be too short?   If that happened, the clutch would lock up when you tightened the nut holding the inner hub. 

 

As Mark said item 2 is two parts which isn’t clear on the diagram.
Here’s a link to the part to make it clear  www.cmsnl.com/yamaha-at1b-1970-usa_model...ngthrust_9334122603/

MarkT I think he’s talking about #18 in the parts diagram behind the basket he says the gears don’t line up. In picture 3 he shows the extra washer maybe I’m confused wouldn’t be the first time 

Ht1kid, you might be right...  the description given says "thrust bearing" and picture is of one of the "thrust washers".

When I think of thrust bearing I think of the flat roller bearing...  and the diagrams don't make it clear that #2 and #3 consist of 3 parts. 

Where you're talking about on the early models there are two washers under the tall spacer.  A 1mm thick and a 2mm thick one.  Those go on first against the trans bearing.  Then tall spacer.  The kick gear and outer hub.  Then thrust bearing (washer and flat bearing) fit over end of spacer. Then one more thrust washer that does not fit over tall spacer.  Then inner hub. 

I looked at some parts and diagrams... 

Should be 4 thrust washers and one flat roller bearing. 

A 1mm and a 2mm washer go on first.  OD is smaller on those washers. 

Thrust bearing washer (not pictured) goes on after outer hub.  Then flat roller bearing.  Those two parts have a larger ID to fit over spacer.  Then comes a thick thrust washer again with the smaller ID but with a larger OD than the first two washers that went on.  You have to be careful so thrust bearing doesn't slip off end of spacer when installing and tightening inner hub. 

Last tip is friction discs are 4mm thick on early model (they sell 3mm thick versions too) and the stack ends with a steel plate on last.  (many parts diagrams show stack ending with friction- wrong) 

MarkT is correct. 

Sorry I meant thrust plate washer not bearing, #18 and #19, when I reassembled I left out one of those thrust washers, the thicker of the two which I believe is #18 and the extra ball bearing (there were two between the clutch push rods when I disassembled) which made everything line up way better. 
As you can see in the pic from the service manual it only shows one thrust plate washer.

The service manual I have is for an at1-c and mine is an at1-b if that's makes a difference.
anyways I've been at work all night. I'll definitely get some better pics of what I mean tomorrow.

If you are using the picture in the manual to identify the correct assembly as the bike was made new, removing a washer is not correct.  The correct service manual is in the Tech Library. 

As far as I know, the initial washers went from two to one on the 1972 AT2 and CT2.  I believe the change coincided with a new kick start gear part number.  Those gears under the clutch did break on the early models so someone could have replaced yours with one from a later model?  And yes, they did remove the 2mm washer in 1972.

So "by the book" the washer removal is wrong.  But in reality if parts were changed it may be the correct thing to do. 

Having two ball bearings in the pushrod is definitely not correct.  There should be only one 1/4" ball bearing.  (I mentioned the size because the one in your picture looks small but hard to tell in a picture) If you need a new ball bearing, check a bicycle shop or Amazon.. you can buy a whole bag for less than one from Yamaha.  Bicycle shop might give you one free.   Same size ball is used in bottom of steering head so having a small bag of spares comes in handy. 

Note that there's also a ball...  but I believe it's a 5/16" ball ...under the shift detent plunger spring.