I recently did an auto to manual swap on my 98 civic hatch which originally came with cvt transmission. The axles can be reused however, the tripod bearing do bot fit into the manual transmission properly because they are too small. Can the cups on the auto tranny be used on the manual?

 

You're doing it wrong. Do not take the joints apart. Pry in between the cup and the transmission and pull the end of the inside joint out of the transmission, and remove the axle with both joints as a unit.

Often a used transmission will come with the "cups" from the old axles still in it. This is because:
1. It is easier to rip the joints apart than to pull them out.
1a. There is no market for used CV axles.
2. The stubs keep dirt out of the transmission.

If your transmission was like that, remove and discard those old axle cups.