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All right, I went ahead and rebuilt my suspension considering everything was worn out. I used upper and lower control arms and all the tie rod ends from O'Reilly's (MasterPro). While I was under there I noticed that the sway bar end links and bushings were deformed and worn, so I changed those out.
The clunky front end is confusing as hell to me. All of the front end bushings and ball joints are new, and if I hit bumps with a little vigor it rattles. Under hard braking to a stop there is a loud clunk from the front left. I have shocks on the way (Monroe Reflexes for the front, Sensatrac load adjusters for the rear), which are the only things left that have been removed and not replaced with new ones.
The truck was perfectly clunk and rattle free with the old worn out bushings and ball joints. I can't imagine why it would start clunking now with a new front end. I felt the new ball joints and they were tight and didn't have any play. The bushings were tight. I'm at the end of my rope with this crap. I've double checked that the ball joint and chassis nuts and bolts are all very tight.
I have identified the source of the noise. It's the upper control arm bushings. They are meant to be a press fit and immovable, but as the suspension acts, the upper control arm is rotating around its bushing, causing the noise. The rubber builds up spring tension until it overcomes the friction of the press fit, rotating violently with a pop. This is why every time I hit the brakes hard it pops once or twice, and why quick corners or sharp impacts make a clunk - the suspension is doing what it is supposed to do, except the bushing is slipping.
I contacted O'Reilly's customer service and they said the district manager will be in contact with me. They stated their parts aren't warranted for labor, but it's completely unnecessary for me to pay for two alignments after spending that much money defective parts.
For those that care, the district manager contacted me and said he'd refund the money for the second alignment after warrantying the control arms. I said I wouldn't mind getting the Moog vs the MasterPro to prevent having to do this all over again, and after we hung up he called me back a couple minutes later and offered to give me a free upgrade to Moogs, which comes out to be a $70 difference from O'Reilly's (online the difference is negligible). Then he's throwing in a $25 gift card to boot.
Not too bad as far as customer service goes. I'm going to try marking the camber bolts positions on the frame with white-out and putting them back where I got them. As long as I mark them they won't change, and the camber alignment spec has enough wiggle room that it'll still be well within the specified range.
Glad you found the issue and are getting it resolved. If the noise continues, try checking the idler arm. Mine went bad and yet functioned fine, but would make a lot of noise going over bumps.
I put on the moog and the noise disappeared. One of the bushings on the masterpro upper arms wasn't exactly a press fit. I could move it side to side by hand easily.
I actually used the truck to pick up a car from Dallas today - a 3800 lb car. The poor V6 definitely shouldn't be towing too much that weighs more than the truck, but it's a solid acid test for my work in rebuilding it. It didn't have any issues when I pinned the throttle to keep highway speed on a couple hills.
I had a similar problem in my 2001, which has already had a few front end parts replaced. I noticed a "clunk" coming out of my driveway, so took it to my front end shop.
They sadly told me my front end was OK, but my radiator core support was rusted out, the radiator was making the noise because it was bobbing around as I drove.
Fixing that was a major problem. I was lucky I was able to do it myself, paying a pro would have cost about $1700 in my area.