Parm and Dado have pretty much covered the common weaknesses of E39s but I see that you have a 6 speed. The clutch is reputed to be weak on the 540s but the 6 speed tranny is quite strong, the only thing that I recall about the manual tranny is that the bushings in the shift mechanism may expand and make the tranny hard to shift, I'm not sure how often or easy/expensive this is to fix.
... oh yeah you should check the valve covers and valley pan gasket for leaks... happens on all 540s.
'99 E39 540iT
Last edited by MLue1; 12-23-2009 at 02:57 PM.
Reason: adding info