The cooling system weaknesses is the same as your e46. So pretend it is the same.

CV boots are iffy and there is thread about replacing them in 30 minutes, teaching some shortcuts that work most of the time. So plan on doing those. GNK is best choice for boots.

You will have the same vacuum issues you had with the e46. Basically regarding the engine, ignition, vacuum stuff, just assume it is your old 330i.

Tranny should be fine, although your fluid is old. Depends on which camp you are in. Change or never change?

Rear sub frame bushings could bite you in the future, but you are probably a ways off from that. Same with the suspension , but since it is heavier it will wear faster.

I would change the front and rear diff fluid(75 90) and transfer case fluid( atf) when you get it. The transfer can be rebuilt, unlike the e46 xi transfer cases. The drive shaft is not long enough and that will bite you one day.

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2001 E53 X5 3.0 Auto. Silver Black Build date 10-17-2000 141kmiles

2004 E60 545i Sport 6MT. Black/Black Build Date 6-2004 102k miles