I did the front pads and rear rotor/pads on my mother-in-laws 04 v8 a few weekends ago. In talking with her the other day she mentioned that every now and then she will get a shaking in the steering wheel when braking, but only when slowing from like 60 to 40. Below that it goes away, and isn't consistent. It may happen just once a day. I gave it a test drive but was unable to recreate the issue. Any thoughts?

I've done some research and because there were no noticeable issues prior to brake job I don't suspect it is due to bushings, ball-joints or cvs, but it could be. Everything felt tight but I didn't do a super thorough inspection. Also, besides rear pads being worn to the metal and starting to gouge rear drivers rotor, i didn't see any indication of stuck caliper or uneven pad wear.

The one thing I am leaning towards is that I think the pads we put on the front were ceramic (carquest wearever platinum ceramic) and I would assume the rotors were standard steel rotors.

Could putting new ceramic pads on old steel rotors cause a problem? I've done some searching and it looks like there could be some sort of temperature related uneven distribution of the ceramic coating that occurred during break-in (no real break-in process was followed) which might explain the intermittent nature of the vibration.

If this is in fact the case. Is there anyway to re-coat or redistribute the ceramic coating?
Will the problem eventually go away?
Should I just replace the rotors with new ones?
Do I need new pads as well?
Should I put semi-metallic pads back on?

I'd like to do the job just once more.

Any suggestions?

does the pedal vibrate also or just the wheel? I just replaced both front axles for a similar vibration (wheel only)

A few months back I changed my front OEM pads (no shaking, but thin) with locally available "American Black" metallic pads ( I suppose somebody is going to set on fire a couple of buildings because of the name) and resurfaced the original OEM rotors (they looked like new after).
Did poor break-in. Couple of weeks later same problem as yours, steering shake (not brake pedal) when breaking down from around 40mph.
Shaking didn’t go away so after 2-3 months, new Brembo rotors and Akebono ceramic pads with proper break-in (empty streets due to COVID).
Since, now 2 months later there hasn’t been any shaking. Improved breaking.
Got the feeling proper break-in made the difference.
Maybe having resurfaced again the original rotors and proper break-in would have fix the problem.

I have a similar vibration when braking. Thought maybe it is worn rotors. Hopefully it isn't too involved.

Sounds like front rotors are bad. If it happens only sometimes it may be only after the rotors have heated up. I changed my front rotors and pads and a few months later developed intermittent vibration. The difference is mine was vibrating without braking. Sure enough it was a sticking caliper. The calipers are a real common 4Runner problem. I've changed 3 out of 4 in past year.

FWIW, I'm like 99% certain that the 4th Gen OEM pads are ceramic, so that's not likely your problem. It's a simple bad interface between new pads and old rotors...unless the intermittent vibration was there before and your M-I-L hadn't noticed because she wasn't paying special attention until you touched her truck. Without putting them on a dial indicator, you'll never know for sure. Same work plus a few bucks just to go ahead and swap the rotors before the new pads get mated to the bad rotors.

I went Akebono Ceramics (possibly the OEM for Toyota) with Centric rotors, myself when I got tired of a brake vibration that showed up before I even hit 80k. I think my "warped" front rotors were caused by letting the dealership do a few tire rotations where they likely applied uneven and/or too much torque to the lug nuts. I hate letting anyone touch my vehicles for service...

Good luck.