It goes away when the air pump stops? Ever considered it might be the air pump? Pumping.

As to the secondary bearings, they can be changed without opening the box. Just drop the rear section off and disassemble. I recently did this. Requires some tools and some heating and is probably best left to your mechanic. You need the three (IIRC) bearings in the secondary housing and the rear seal.

Turned out to be my diff however. :banghead:

See this thread for all the details:
http://www.s2ki.com/s2000/topic/7948...#entry19066562