94' Honda Civic

My girlfriend broke her CV half shalf on her 94 honda civic ex auto trans two weeks ago. So I replaced it for her. She has 170000 miles on this car and has never had a problem with it. The CV half shaft was a pretty easy thing to fix or so I thought. I disconnected the lower control arm, pulled the nuckle out a little ways and I was able to safely remove and install the new shaft. I was excited and took the car for a test drive after refilling the transfluid. All seemed great. 2 days later a loud rumbing noise similar to when a caliper is sticking to the rotor started appearing. I told her to ignore it because I had noticed the calipers were bad when I had it all apart. Then I took it for a ride agian and noticed this was no caliper noise. I jacked up the whole front end put the car in nuetral and spun the front tires. The noise wasn't coming from the rotors but rather the transmition casing. The noise is hard to describe but it changes during the rotation of the shaft. If you go very slow it is kind of a growling scrapping sound for the first half revolution then a sort of a klunk followed by a smooth rotation for a quarter turn. Almost like a warped rotor except I am certain it is coming form near where the CV shaft enters the transmition. What have I done in this fairly simple repair and can it be fixed? Oh yeah it still seams to drive fine if your ok with the entire car vibrating and the loud noise. But it still shifts when it is supposed to without any difficulty