Rough transmission, possibly caused by axle removal

[AlphaAssault]

So I finally got my car running today, and I decided to drive it to a place where we could get the drivers side inner cv joint off the car (I just pulled the axle shaft and outer joint, leaving the inner end in the car because I couldnt get it out). Now, heres the deal, I noticed the transmission is worrisomely rough: Shifting into each gear results in a very vague grinding, and when letting the clutch pedal out I could feel vibration from the car until the clutch was fully engaged. I could avoid those vibrations if I accelerated veeeerrrrrry slowly, but they were present upon normal starts in 1st gear. I dont remember feeling the vibrations in any gear other than 1st.

What could be causing this??? It feels like something isnt quite aligned anymore. Could all that banging on the inner CV have messed up my transmission some? Hit me with some ideas here, i am prepared for the worst

I feel horrible, i think im going to be sick...

 

[AlphaAssault]

Just had a thought: if the spindle connecting the driver side axle to the transmission was pulled outward a little bit, would this cause the symptoms I am describing?