Can't pull out clutch push rod ?

i'd say remove the inner hub first and then try it  
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03 rm125

2stroke eff tee dubba u

well yes, this was my recomendation, take the clutch off the bike, not hard to do, and it will make things easier and might fix the issue altogether. i have a feeling he hasn't replied back because he is working on it and has probably fixed that issue.  
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Whole clutch assembly fully removed:


Here you can see those few milimeters of the push rod, it doesn't come out any further.


And here is the damaged bearing because of which I am splitting the cases. I have never done this before.


To begin with, I am from Lithuania (Baltic countries) and we still don't have an official Honda dealership.

I tried to move push rod counterclockwise and clockwise, backwards and forwards, didn't help. I doubt that there is a vacuum created by gathered oil. Push rod moves freely about 1/2 inch forwards and backwards but doesn't fully come out.

So, I haven't fixed it yet  

Where are the damaged bearing peaces?  
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I love this dirt stuff.

Some pieces I took out, other are still with the bearing. Crank is turning freely so I hope that the bottom end is still ok. I bought this bike not knowing when was the last time main bearings were replaced. So this is a good lesson for me, I would recommend everyone to change crank bearings if it is not known when the last service was to avoid such problems. Bearings also damaged the crank seal which damaged the spacer on the shaft.  

Hmmm. I'll have to research this a little and get back to you.  

Found out what was wrong someone, who rebuilt the engine before me, put the rod in backwards. It turned out that the rod has some lip on one end. It was put wrong and that lip didn't allow the rod to slide out.
Here's that rod lip:


While splitting the cases I had problems with countershaft. According to manual, before splitting I had to remove a collar from the countershaft end where sprocket goes. However, I couldn't remove it as it was stuck (maybe because of rust). So I split the cases and countershaft remained in it's place.

I tried to hit the countershaft with a rubber hammer but that didn't help. Now, how could I remove the collar and the countershaft from the crankcase?

 

ial be damned
it was in backwards...  
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1998 cr125
its better to own nothing worldly and still have your identity
then have the world and no identity
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Also, I found a Hot Rods crank rod which is good I suppose The main bearings were different! One of them Koyo and the other NTN. The Koyo blew up and the NTN was still good but rusted and hardly spinned.

Any ideas on the countershaft removal?  

So finally I replaced main bearings and put the cases back together. Now my concern is the gearbox. I am fairly sure I put the gearbox correctly. However, when I assembled all the gear shifting mechanism and put on the gearshift lever, it's quite hard to shift through the gears. Could it be because there is still no oil in the gearbox or something might be wrong? I can shift into any gear including neutral but it takes some effort. What do you think guys?  

I wouldn't judge anything till you fill it with oil and run it a bit to warm it up. Take it easy and let it warm up in idle for a few minutes then just take it for a ride around the block sort of thing then bring it home and give it a good going over. If theres any major problems you'll find out very very quickly but just listen for any strange noises and pay attention to how it shifts once it warmed up a little. Sounds like you did a good job though.  
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