I'd think that if it does the same thing with the new alternator as it did the old one, check the connections at: back of the alternator, jump start connection positive post, engine ground. I have seen it before where the engine ground cable (at passengers side motor mount bracket) had a funky connection and caused a poor charging output and weak starter due to lack of ground path.

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X5 pics

RIP 4.6is.....

2003 4.6is