I ended up buying a very clean looking looking, long runner intake on Ebay yesterday, PN 11611729528. This pn coincides with what RealOEM lists as the OEM manifold for the 4.6, and which it seems was installed on a earlier M60/62 engines for many years.

After connecting with some knowledgeable E39 guys on the other forum, it seems that the M62TUB46 will run on any of the three intakes out there, but will run best on the xxx9528 intake. The gold standard seems to be the oldest of the M60 manifolds, which has velocity stacks on the runners but may need some modification, depending on application. These seem to be identifiable by one less (front) mounting point for the fuel rail and the absence of the small internal molded bracket/hole for the CCV vent pipe that runs from the valve back up to the front of the manifold. It also looks like there may be one less mounting point for the throttle assembly, but the photos I've seen aren't that clear on this point.

All three were available, as well as 4.4 intake options, so I grabbed the long runner manifold that is 100% common with the 4.4 plumbing and CCV set-up, and if RealOEM is to be believed, came on the 4.6is. This will make it much easier to order parts and consumables like O-rings, etc. and quickly swap pieces over from my 4.4 when the time comes.

The production dates for the xxx528 manifold in RealOEM don't add up with the 4.6is production dates, but perhaps its an error. Short of someone with a stock 4.6is looking at the PN on their manifold, who knows. The good news is that it seems that e39 guys are running all versions of the long runner intakes on M62TUB motors, with DME tunes and without.

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Current
Original owner 2002 E53 X5 4.4i to 4.6i swap
2026 G80 M3 6 spd
2025 G06 X5 50e
Former
1972 Audi Fox
1986 Saab 900S
1996 BMW Z3
1998 BMW E36 M3 Sedan
2004 BMW E46 M3
2006 Audi A3 Quatro
1993 Mopar 318 Jeep Grand Cherokee
2015 V6 Jeep Grand Cherokee