1) Decide which set of rockers are best and use them on the 4.6 heads, keeping pushrods matched to the rockers. Definitely leave the tappets in place, as these are worn to the cam, putting mismatched ones in can munch through the camshaft very quickly. You may want to check the perload on the tappets as you are fitting a lower head, if too much then you fit shims under the rocker towers until correct. Google for this, it's described very well in many places.
2) You could open up the exhaust and inlet ports to match the gasket line, but even this is time consuming, will easily take you a day and a set of ringing ears. also remove any extra aluminium from the valve throats and feather it to the inlet tract (though this will require removing the valves....) Anything more than that is probably not worth it.
3) I don't see an issue here at all, just rinse well after as most cleaning chemicals (caustic!) like to eat aluminium slowly.
4) Sorry no, but the top end (inlet manifold etc) is a very straight forward swap, using the same bolts.