1998 Honda Accord Clunking Noise

I have recently replaced both front upper control arms (ball joint issues), all four struts, and all four sway bar end links. This work has all been done in an attempt to fix clunking noises coming from both the front and rear suspension. Initially the problem was only in the front. The noise sounds like a hollow clunking, especially when going over dips in the road or slight indentations in the pavement such as manhole covers on asphalted roads.

First I had the front struts replaced which didn't fix the problem. Then I had the front end links replaced which seemed to almost fix the problem. Finally, after taking the car in for an alignment, the front upper right ball joint was determined to be worn and so the control arm was replaced.

After this work and an alignment, the car pulled to the right but the clunking noise was completely gone. I had old tires on it so I just let the pulling go because I planned to get new tires soon and figured that might be the problem.

In the meantime, the rear started making a remarkably similar noise. I had the rear struts and rear end links replaced at the same time. This of eliminated the clunking, but it came back in a couple weeks, although not as bad. I've been meaning to schedule an appointment to have it looked at some more but haven't gotten to it as of yet.

Then, the other day on my way to get new tires put on, the front left suspension collapsed. I had to replace the upper and lower ball joints and the left axel.

So, after new tires and this work another alignment was done. Since it seemed that the worn ball joints on the front were related to the front suspension clunking, I asked the shop to check the rear ball joints when they did the alignment (this car only has lower ball joints in the rear). They didn't notice that they were worn. Also, after the alignment, the car still pulls to the right even with new tires.

My questions are:
1) what could still be causing this pulling and
2) what could be the cause of the clunking in the rear? Could it be the ball joints even though they didn't appear worn?