This is exactly like my truck.
Except mine is an 06, 5-speed automatic, TRD, SR5, with fog lights, wide fender flairings, a high camper shell, different wheels and it is gold.
Right around the time we zipped past 45,000 miles I began hearing some klunking sounds up front. Today we are at 46,660 miles and the sounds are getting louder, more frequent and more pronounced.
None of the sounds is duplicatable. They happen rather randomly.
The lighter is a solid metallic sound that occurs when I first start from a stop. I guess this could be the brake pads shifting and hitting the stop-pins.
The heavy sound is much deeper in tone and it reminds me of ball-joints failing. It also reminds me of the loose inside of the steering rack I had on the old Dakota.
Dex and I spent quite a while peering around with flashlights last time it was on the rack. Everything is clean, pretty and looks perfect. We shook, twisted prodded and poked. He used a pry-bar to check ball-joints. Nothing.
I use and talk about, but don't sell Amsoil.
Who is shatto?
06 4.7 Tundra replaced a 98 Dakota 3.9.
623,000 miles on original engine and transmission, using Amsoil by-pass filters and lubrication.
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The brake pad movement thing is not happening. If there was enough slop between the caliper and the pads, you wouldn't be stopping.
Crazy idea. Take out the 30 weight non-detergent oil and put in the oil recommended by Toyota along with a new filter.
A noise when coming from when you accelerate away from a stop sure does sound like an engine problem. So does loud muffled noises after you were talking about what you were doing to "solve" oil consumption.
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DO NOT WAIT to deal with the ball joint noise. Toyota has had repeated problems with ball joints (IIRC they were getting scratched during manufacture) and has recalled a lot of them. On my dad's 2002 Tundra, a mismanufactured ball joint failed and folded under the truck while he was driving. If he was on the highway it would probably have rolled the truck. Even if your VIN isn't listed in any ball joint or suspension recalls, it should still get special attention.
The best way to check ball joints is to put a load on the suspension without involving the tire and wheel. Usually this means jacking up the vehicle using the lower control arm close to the ball joint that you suspect is bad.
Otherwise your testing is fighting the springs (whether it is a torsion bar or a coil) pressure against the control arm and the ball joint.
This applies to both upper and lower ball joints. In most cases the play in the joint is easy to feel as long as the spring tension on the suspension is not fighting you.
For tie rod ends (both inner and outer) a good way to check them is to rock the steering wheel back and forth while holding your finger between the socket and ball, with the vehicle on the ground and not running. By rock the wheel I mean just enough to feel significant resistance, not enough to really move the wheels any significant amount or smash your finger. The play would be felt between the socket and ball and should be fairly obvious.
Another suspect is the sway bar. In some cases it may be best to just remove the whole sway bar assembly and drive it for a couple of days.
I would not think it would be the brake pads when you accelerate, because they have no real tension on them, without pressure in the system, as there is when you apply the brakes. A good visual inspection would be a good idea at that mileage.
A bad motor mount can also cause that sound on acceleration, with all the other trouble you are having I wouldn't be surprised if a mount is loose or ruined. One person in particular I've known had about 60k miles on her fairly new focus and it had a raped motor mount.
Check the trailing arms and the brackets that they bolt to and all chassis bolts and nuts. Scion has a 5000 mile interval check on the chassis bolts and nuts and of course they don't give a torque spec. Also try backing up and applying the brakes hard aand then go forward and apply the brakes and see if the clunk is there.