Good choices... the e39 and e46 are some ofthe last of the relatively uncomplicated BMWs.
e39 with the 3 liter has all the same issues as the e46 with the 3 liter. The 4.4 V8 is pretty reliable but I believe all the V8s of that era have an issue with the alternator bracket leaking oil. It's a 9 hr job by the book but it can be DIYd, it's just a PITA. Valve cover gaskets are the typical BMW. Suspension has the typical bushing issues.
Stay away from the air suspension.When it goes bad, it's a nightmare to fix.... we've spent thousands on the air suspension on our X5 and it's still not fixed.
Dinan CAI &Throttle body, ESS Tuning TS2, Bimmerbrakes gen3 headers, UUC SSK & DSSR. Achilles oil pump, VAC oil pan baffle
M3 Motor mounts, UUC Trans mounts, Modified clutch style LSD 3.15, TMS front subframe reinforcement, Koni Yellow sports,
H&R sport springs, UUC sway bars, BMW Perf. Rotors, UUC SS brake lines, Hawk HPS pads, CSL replica wheels,
Rotora strut bar, FXR HID conversion, M3 Mirror conversion, BSW stage 1 speakers