I don't think you want the ball housing full of oil. When you get everything back together you should pour about a half cup thru the small hole at the end of the transmission. This will lubricate the u-joint until it starts to come in from the trans. Was the inside of the ball housing scored from the u-joint hitting it? If it is then either the u-joint is sloppy or the gap between the collar and the ball housing is too tight. The gap between the two is crucial and although I don't know how the 41 compares to my 49, I would think they are alike. In my shop manual there are directions for determining the gap, which is set up with carboard shims. It is too long to go into here but when I did mine I used 4 shim/gaskets between the two pieces. Too tight and it will bind the u-joint and too loose it will leak. With 4 I was okay and I have just pulled it apart again to install the okie bushing assembly. The idea behind having multiple shims is that if it starts to leak at the joint you can loosen off the bolts and tear out one of the shims.
If you are all apart I would suggest to err on the side of caution and change what you need to. A friendly transmission shop should tell you if your u-joint is good. And if nothing has been done to the bushings in the TT then an Okie kit would be a good idea. However do not believe all the ads about the Okie job being done in an hour. I finally got my front bushing out today and that alone took an hour.
Bill
