NO, NO, NO! Hammering in a crank, are you guys nuts? That's a great way to f**k up a crank!
Listen to me gerumgoingoingboing or whatever the hell your name is (lol).
First of all I believe you have no spacer between the right side crank bearing and the primary gear.
Either that, OR you have an incorrect spacer. The spacer should be 12,6 mm wide.
EDIT: You might want to check so that the biggest gear on the crank (the gear for the balance shaft) is sitting correctly. If I remember it correct, it MIGHT jam against the case if you put it on backwards. The way to tell if it's sitting correctly or not, is if you can see a marking at the teeth. This marking should obviously be lined up with the marking on the other gear that is located on the balance shaft.
Secondly - as for THIS particular problem you have encountered, it wouldn't matter if the cases are mismatched, as EVERY RD125 crank have the exact same width where the main bearing seats (unless ufcourse the crank has been rebuilt and not pressed together enough, or if it has been pressed together too far).
If you have a problem with the bearings then honestly, the best thing to do is to stop f**king around and do the job again, this time properly.
1: Take the engine apart again. You shall be left with an empty left hand case. It should be ENTIRELY empty, in other words; no seals or anything heat sensitive in it.
2: Put the crank and left side main bearing in the freezer until the bits are ice-cold.
3: Put the empty l/h case in the oven at about 120 C.
4: Take the case out and put it on the kitchen table.
5: Take the left side bearing out from the freezer and drop it into the case (you might want to have some paper at hand, to wipe off the condensation that will quickly build up on the bearing). This part can be tricky. If the case is not hot enough, or if you manage to get the bearing in a bit "unstraight", the bearing might not fall in all the way. If this happens, DO NOT try to force it in. If it doesn't fall in, just knock it out and put it back into the freezer again, warm the case up again and add a bit of extra heat - then try again. It SHOULD fall in all the way with NO effort if you do it right.
6: Now you should have a set of cases with both bearings nicely seated in place (I have so far ASSUMED that the right hand main bearing is already in place). Put the left side case back in the oven and take it out when warm.
7: Drop the crank into the left hand bearing. Make sure to get it in straight and quickly. It should fall into the bearing all the way, just like the bearing fell into the case earlier.
8: Now you're pretty much done. Just sneak the gearbox assembly etc into the left side case, clean all the mating surfaces and add Yamabond or whatever you're using (Yamabond is recommended).
The right side crank bearing should not have a press fit over the crank, which means that you can just slide the right hand case, including all the bearings, over the crank and all the other shit that is sitting in the l/h case.
After this is done, lube up the seals and pop them in and... yeah you now the rest.
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PS:
A tip for the right side crank seal, is to first put the spacer that I believe you're missing into the seal. Then slide the spacer and seal on as an assembly.
Make sure that the spacer DO NOT fall out of the seal.
Believe me - you DON'T want to push the seal into the case first and THEN try to slide the spacer into the seal, as it might prove to be a pretty goddamn impossible task hat can easily f**k up the seal.
Don't ask me how I know this.
,the width of the bearing was too thin so the crank pulled up to the side of the casing and not the bearing.