First, and in my opinion, the easiest to check, would be the transfer case mounts. I just did this on an e46 manual we just bought and though they looked fine, they were actually sheared off at the top. Throw it on your new lift and grab a prybar and try to lift the t-case. $20 bucks and about 30 minutes later, no clunk!

Good luck!

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2004 X5 4.4 Build 01/04 Alpine White on Schwarz Dakota Leather, Anthracite Headliner
Xtrons Android HU, SPORT PKG, COLD WEATHER PKG(W/REAR HEATED SEATS AND HEATED STEERING WHEEL), CONVENIENCE PKG, FACTORY HITCH