So, here's what I've heard so far;Electronics and induction are basically the same. The 4.6 intake is the same piece that Dinan sells for the M62TU and BMW installed on the M60 engine.
The biggest challenge was the oil pan and crankcase ventilation system as the truck and car systems are different. Alot of small parts need to be changed including the oil pump, pump chain, oil pan and valve covers.

Software is another story since BMW never put this engine in front of a manual trans. An automatic car would be a piece of cake.

Engine mounts bolt to the block using the same holes, no problem there.
Accessories mount the same also, no problems.
Wiring harness connections are all the same, assuming that the E39 has an M62TU engine not an M62. 4.4 and 4.6 DME's are the same basic hardware number. X5 software does not perform well with a manual transmission.
I.m using 4.4L m62tub44 w/automatic transmission so, all good

Parts list is kind of extensive. Mostly to fix differences with the oil pan which shouldn't be too difficult to replace with an e39 pan and plumb for pumps and cooling.

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'03 4.6is (the wife' s ride)