I just put my motor back together and i noticed the depth of the stator side seal
On a spare block. I made my seal almost flush and i was wondering if i should take my flywheel back off and set it deeper. Will it leak or lose big time case pressure if i leave it?
Service manual says to set the depth of the seal at 5mm on right (flywheel) crankcase half, 1mm on left crankcase half on the '94-'01 SA50's. Why the different depth settings? Might have to do with the tapered end of the crankshaft? Maybe some others will give better info on this subject being yours is not a stock motor. Good luck with the project. Hope this helps but you can see for yourself here: http://www.hondaspree.net/other/SA50_88-02_service.pdf
Keep in mind that that's for oem honda parts. 1-2mm below the lip is good.
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I have learned why it should be set almost flush on the pulley side. I had set the seal too deep and the oil pump gear chewed up the seal. On the flywheel side there is a stop point and you can set it all the way in to that.
Always do physical and sound checks followed by pressure and vacuum tests. If you heads some odd rubbing or scrapping do not proceed. You'll never have a fear of it leaking if you do the tests that take minutes.