As you suspect, an alignment won't fix a clunk noise. Sounds like a simple case of misdiagnosis. I'd tell them you don't want to get the alignment done until they find/fix the actual problem as the parts replacement will likely need an alignment after as well. And if they still insist on having the alignment done first that the next alignment will be on them...

I know if I were to missdiagnose a car it all rolls back to me, I would end up doing free labor and either have to put back the old parts or pay for them. (what a shop of 25 techs has to do to keep the newer techs in line because if the shop ate it they'd never learn and wouldn't care about work quality) In my early days, before I knew the BMW systems inside and out, I had to cover parts cost and do free alignments in a case like this... may have cost me some time/money, but it kept a really good customer relationship and was good for the customer and company/shop. That particular customer was the first to start requesting me to personally work on the vehicle on all their return visits as they then knew the level of work ethics and work quality to expect.

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"When you do things right, people won't be sure you've done anything at all" (Bender, futurama)

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RIP 4.6is.....

2003 4.6is