wineing noise from 2nd gear

My friend has a bike (2003 CR 125) that just recently started making a whineing/grinding noise from the tranny and it is only in 2nd gear when there is load on it... both me and my dad think it sounds like a bearing going bad... is there a bearing or something linkeed only to 2nd gear? also one of the crank seals is leaking making the oil really black and smelled like cumbustion even after 1 hr of run time and making the bike has nothing for bottom end power... we changed the oil there was no chips or anything in it and put in fresh (honda HP2 gearlube) and it still makes it.
we were planing on taring the bike down pretty soon anyways from the crank seal going bad so i geuss now we have 2 things to deal with.

Anybody? ... ?

is there any body out there