Just got finished with a 4.6 rebuild in my 04 D2. I would reccomend using the ARP Head studs instead of bolts. During assembly one of the head bolts pulled the threads on the block. Ended up heli coiling it so its fine but I would recommend using the studs.
Check out D&D Fabrication's web site:
http://www.aluminumv8.com/
Call Mark at D&D and ask him about his cam and timing sets. We installed a crower cam and timing setup thats much better than stock. The motor gets into the power band lower in the rpm range now and keeps on pulling and pulling. I would recommend anyone building a Land Rover motor to contact Mark at D&D and pick his brain a bit. Very knowledgable.
While you got it apart....go head, as previously reccomended and port match the heads to the exhaust manifold. On my Bosch motor, you wouldnt believe the burrs and metal we polished out on the intake manifold, if its a bosch motor i would do that. Gems motor you typically shorten the trumpets.
After all the motor work I done, I would say my truck is much better than it was new!
Good Luck
Justin