so I am in the process of replacing my transmission on an 87 samurai.  I have my old one pulled out and am ready to put the new one in, but was wondering if i can just put the gear oil in through the top since i have the shift knob out at the moment, rather than have to pull the fill plug.  once it is installed that is haha. 

Put it in through the top for sure... Much easier.

Pull the fill plug from the side though so that when the fluid begins to trickle out slightly you will know when it is full. Also make sure you use GL5 Yellow Metal friendly fluid.