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The lower than 14.4v charging could be lesser RPM that the alternator needs. Being it from a different engine, have you compared the pulley sizes?

http://www.nissanpatrol.com.au/patrol-manuals.html

Have you downloaded the manuals? There are pretty good diagrams to read. You might have to test the existing loom for open circuits or incorrect wiring. If it is such a mess, I would probably rip out...

I have seen the Patrol doctor system, where the they use a stainless snorkel and airbox fitted close to the passenger firewall. Maybe have a quick search online to see if they suit your needs.
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