I recently changed out the brake pads on my 07 IS250 AWD and 10 minutes after bedding in the brakes I realized there was an audible clunking/clicking sound from my passenger rear wheel area especially under acceleration at speeds >40km/h.

The sound persisted for a couple of days until I brought it to the shop for a diagnosis - apparently the repair tech told me the CV axle boot was torn and flinging grease everywhere - but due to them not being to source the replacement right away I didn't get it replaced yet.

Fast forward to today, I haven't been able to hear any noises coming from the area for about 2 days now. I doubt any mechanical issue could have fixed itself so would someone here be able to lend me some insight or advice?

I would recommend to get back down there and look around. Start by taking the wheel off again and looking around. Is there anything that looks out of place? Check to make sure the caliper and bracket bolts are tight. If the shop said your axle boot is torn then take a look. There's no reason you shouldn't verify that the boot is actually bad before having someone replace it. Also, check that the sway bar links aren't bad. Are they broken? Can you "twist" or turn them back and forth? Make sure they're screwed in tight as well. You should also make sure that all of the brake clips and retainers are properly installed. The dust shield could also be bent and rubbing against the rotor. Just some suggestions, as I don't make any claims of being an expert.

Thanks TopNotchIN, I'll definitely give those parts another pass over.

The boot was probably bad before the brake job. I'm guessing the braking components used (or those that were not used) are to blame. Did you reused the OEM brake shim AND the anti-squeal shim? Did you also install new OEM brake hardware (slide pins, clip) by chance?

If the old shims weren't used what issue would that cause.