update
 

Replaced the sway bar links today and the clunk is almost gone but not quite.

There is now no clunk sound when driving over small bumps (e.g. sewer covers about 1" below the pavement). When hitting a ~2.5"+ bump, I do hear a front clunk but seems to have a different deeper sound now.

Still can't feel any play in the old sway bar links on the bench but the new parts definitely helped so they must be worn.

So I think there is/was more than a single issue causing the clunks.

Next on the list are the tension/control arm bushings.

For the GTA owners, I bought my parts from Germanparts.ca in North York (no affiliation, just a happy customer)

FYI, I was at 92k when the clunking became noticeable. '08 3.0Si.

It became progressively worse over the next 1k miles. By 93K and some change it sounded like a slide hammer was in place of the shock. Interestingly it sounded worse on small bumps (man hole covers) then larger pot holes.

I forgot to mention in the earlier post but I ruled out the sway link by removing it altogether and then driving around the block over the same man hole cover that was making the noise happen. No change.

The Lexus dealer replaced both struts, guides, and flanges under their used car warranty. Clunking is gone. Total invoice for the parts and labor was just over 1.9k on their dime. Didn't think the struts needed replacement but a nice guesture on their part. Won't need to replace them again for a long time. Unfortunately the plastic bulkhead supports fell apart during the job that I replaced today. Gladly trade the $180 for the parts for the strut work.