My 94, 3.0, auto has a clunking that is seemingly coming from the driver's front area and its pulling to the left a little. Visual inspection shows everything to be looking fine and I rechecked torque on all front end parts. Tie rod bushings (tie rods were fine last summer), shocks, steering damper, lower ball joints, pitman, idler arm and control arm bushings are all new. Where should I be looking for the mystery clunk? The upper boots look good and aren't leaking, but could they still be bad? Usually, I just replace them when the boot starts leaking...

Lift the wheel off the ground and check it for play. Side to side wobble is tie rod ends (or steering/idler arms), top and bottom wobble is ball joints. If that's all good, look at your control arm bushings.

Well said!

It's hard to find slop in suspension or steering parts with weight on the wheels.

Whats the acceptable amount of play? I get a little side to side, grabbing tire at 3 and 9. Maybe like 1/16" to 1/8". Hard to tell with no way to measure other than feel. Wanted to add too that while driving, steering is nice and tight. I always thought tie rods produced wandering/loose feelings. Grabbing at 12 and 6, I have little if any movement. I'm gonna have a buddy come look at them later tonight while I move it. Having another opinion and watching the joint itself might be helpful. Anything else produce side to side movement? Wheel bearings? I know those were repacked/greased (or something?) when my mechanic did the brakes last year, but not replaced. And finally, if it were the tie rods, would it explain the clunk?

You might consider doing the a-frame bushings along with the upper ball joints. I found when I did the front end on ours, they were shot(with only 70k on them). It really tightened up the truck, far more stable on the highway. Do the tie rods have any play?
regards

A frame bushings = control arm bushings right? Those are new as of last summer. I have a little bit of side to side play. Very minimal, maybe 1/16". Up and down play there is none. Just went out and double checked. So, anymore thoughts on the clunking? Checked drive shafts, just in case. Sway bar bushings to frame need to be replaced and are on order from dealership. Links and bushings are new. Tried yanking that around and got no movement. Running out of ideas to check for...

Ok, so when does it clunk? Under acceleration? Under braking? When turning?

Clunks over most bumps, even smaller ones. Going straight it happens, also while turning. Ride feels a little wonky too. Almost like shocks are bad, but they aren't. Thats why I was thinking ball joint. Feel free to throw out some more ideas. My first step is to get the sway bar bushings taken care of and then I guess I'll start going down the line if thats not it. CVs be the culprit maybe? I've had the hubs locked for the last couple weeks because my driveway it all washed out/muddy. I guess tomorrow I'll try unlocking those too and taking it for a little drive.

Yes, on the control arm bushings. Definitely unlock the hubs, that is probably the clunk. I only lock ours when it snows 2ft, or logging road, and or driveway with 16% grade. You might consider replacing or checking the driveline mounts, they really improved the ride on ours. The motor mounts made a huge difference.
regards

Did the OP ever find out what the clunking was?
I'm having very similar sounds and stuff from my 94 4runner... I'm chasing it down, the last things for me is the front control arm bushings.