A while back my car made a popping noise on some bumps but mostly when turning left. Turns out I snapped a sway bar end link. Put new bushings on and no more clunking.

It actually did pop a sway bar endlink at one point. It was really loose, thought I was going to loose something serious. So I pulled the pass side apart. Soon as I put my wrench (not impact) on the bolt, it snapped and the sway bar sprung. The whole thing had been rusting inside and came apart in 2 pieces. But, those were the old mounts and the old FE1 sway bar. Now it has the FE5 bar and all new moog endlinks.

Here is a theory, and you guys tell me if I'm way off, (yeah, Im always "off" but thats besides the point...)

With this motor mount problem, its been the cause the whole time. The mount was letting the engine torque over and throw the axles and bearings out of alignment. So, even with new axles, they would still pop, since the mount was still bad. (Really bad, like it pulled the intake pipe off the airbox bad!)
Now, the mount is fixed, and that part is good. But I'm still left with the symptoms of what it was doing... ie, the axles that are new are still popping under load, and the bearings are worn out with all the drivetrain twisting and the 300 miles a week I put on it like that. So the cause of the problems is fixed, but the symptoms are still there.

In other words, now I have to replace the axles again, maybe bearings, now that the driveline stays in alignment.
Maybe its something else. I don't know. Im still pretty baffled.

Since you seem to know your way around, pull the drivers side axle, Check your outer trans seal.. then check the shaft

Well, I was thinking about pulling the axle.. but..

One thing I forgot to mention, is I know for sure that the vibrations are coming from somewhere between the trans and the hub. I can feel the brakes pulsate. And I can hear them. When I did my front pads, they came with new guides. Well, the guides turned out to be pretty crappy, and often the pads drag them into the rotors, making a high pitched squeal. Today was one of the few days in the last couple weeks where I could drive home with both windows down, and I could easily hear it. Instead of one long squeal, it would squeal on and off with the brake pulsations. So, something is definitely warped, or throwing the discs out of whack. But, since it happens on and off, and not constantly, I'm starting to think my axles and bearings are all shot now that the motor has been throwing them around. I can also hear two distinct pops. With my windows down, I can hear the usual one coming from the front left, but now I have also heard one reverb off the wall on the right hand side as well. When I backed into my spot earlier, I pull forward, then reverse, and when I put it in reverse, it popped out of the left, then when I gave it gas, it popped on the right.

I'm no genius, and I'm certainly no expert on cars. I learn all I can whenever I can and do all the work on my own whenever possible. But it sounds to me like another pair of axles and possibly both bearings. Since the rotors are moving, if the rotors aren't warped (since they don't always pulsate, I'd assume they are ok), its probably the axles popping around, and the loose bearings are transferring that axle play into the hub, where I feel it in the brakes.

But thats only my guess. I'd hate to be wrong and end up with one more pair of axles in there that solves nothing. The drivers side is easy, the pass side, not so much. Nothing to pry it out against. Had to have a shop do the last one on that side, since I couldn't budge it. The bearings aren't too bad to do, I still have my press to get them out of the knuckle.

I just hate being wrong and replacing these parts over and over again.

You got a Bad wheel ?? One thats bent ???

Remember they are balanced at low speeds..

If it were a wheel, they've been rotated around all corners with no difference.
Wouldn't explain the pop sound either.
And when I am stopped at an intersection, going to pull left out onto another road, I can feel it jerking on the wheel as I first start to roll forward with the wheels turned. Doesn't do the same if I make a right turn though.

sounds pretty logical to me i know i had the same issue with bad mounts messed up my drivers side axle most of the same symptoms

SilverSleeper do you have an update for us?

This thread has gotten pretty long so i can't remember if you had stated that you have had the alignment checked yet. I was having lots of weird steering/suspension issues and kept throwing parts at the problem and finally had the front end aligned and all of my problems were solved. Thinking the alignment had to be way out of spec to have been causing as many problems that I was having but now my 2001 Bonneville with 235,000 miles on it drives like a new car.

Was there ever a solution found for this?
I am having many of the same issues motor mount was replace and still vibrating alot.

Best to post up what your problem is in a new thread.