I did a bunch of work on my Toyota - replaced the driver’s side axle, lower ball joints, rear and front motor mounts - it worked great for about 40 miles, then heard clunking and other noises and limped home. Is there a procedure for aligning the motor properly when mounts are changed (I had to drop all the cross members to get the rear one in)? After taking the axle out another few times (grr) and even putting the old one back in, I noticed the tranny end with the splines, would travel outwards as I tightened the big axle hub nut. I began to think maybe the motor shifted away from this axle towards the passenger side so the axle wasn’t the right lenght for that. The clip on the end of the axle is holding it properly from coming out (I know this FOR SURE!! by now). I checked out the rear mount, and it has some play about where it can be in the holes before you tighten the nuts.
The current plan is to pry the mount bracket toward the driver’s side and then tighten it (engine is being supported right now), to see if this helps at all.
It just seems weird that the axle looks great, until I tighten the axle/hub nut, when it starts to travel out on its splines. Maybe that travel is normal, and nothing to be concerned with, but I just don’t know why it was making scary noises all of a sudden. At least I had 40 miles of bliss- no vibration, nice tight steering…anyone have any ideas - the faster the better, as Mom is coming back this week and needs her car! 
You might want to check that side and make sure the ball joint you replaced is still attached to the steering knuckle.
Tester
The one I replaced is the lower ball joint (end of control arm). It has 3 nuts that hold it on, which I disconnect so I can get the axle through the hub. I put a new axke seal on the tranny and put the splined end in, but was thinking about how that could possible come out again. I noticed a groove in the splines in the tranny for the lock ring, and assume that it locks into there, and doesn’t have to go any farther in. It should take a lot of pressure to pull the lock ring out of that groove, so it’s weird that it must be happening. I’m going to take a closer look, but I don’t think that lock ring goes all the way past all the splines way in the tranny - I think it just goes to that groove, but what do I know??