The 4.6L will have a better chance than the N62 4.8L as the latter was never paired with the ZF5HP from the pre-LCI cars. Also the X drive is different between the two with the 4.8L using the ATC500 transfer case. The preLCI ones are mechanical and the postLCI are electric with an actuator.

Unfortunately the 4.6L variant of the M62 is more rare (and expesive) than the 4.8L. Programming would be a huge hurdle going to the N62 4.8L and would require swapping a lot of modules (harnesses too I assume). I'd stick with building an M62 4.4L up or swapping an M62 4.6L if I found a reasonable one were I in your shoes.

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2005 X5 4.4i Build 04/05 Maintenance/Build Log
Nav, Pano, Sport (Purchased 06/14 w/ 109,000 miles) (Sold 8/15 w/121,000 miles)

2006 X5 4.8is Build 11/05 Maintenance/Build Log
Nav, DSP, Pano, Running Boards, OEM Tow Hitch, Cold Weather Pckg (Purchased 08/15 w/ 90,500 miles)

2010 X5 35d Build 02/10
Nav, HiFi, 6 DVD, Sports Pckg, Cold Weather Pckg, HUD, CAS, Running Boards, Leather Dash, PDC, Pano (Purchased 03/17 w/ 136,120 miles)