OK, so I'll speculate on a few things here based on what I have learned from building spacecraft that depend ENTIRELY on conducting heat to radiators that look at cold space to maintain their desired temperatures. This is speculation, though, and we would need to do some careful testing to verify.
First keep in mind that your whole engine is pretty much a big chunk of heat conductive metal, generally iron or aluminum. There are a few "heat breaks" in the system, basically intake/exhaust/head gaskets. The manifold gaskets are pretty thin (plus some have metal cores anyway), so probably (would have to test to know for sure) they don't provide much of a thermal barrier. Good thermal conductors (most metals, the exceptions being most stainless steels and alloys of titanium) in general don't tend to allow much in the way of temperature gradients: even with the forced air (preheated by the water radiator, oil cooler, etc.) going through the engine compartment I doubt you get any more than several degrees F gradient between spots near the top of the block or head (excluding the manifolds which are a special case). I assume that a thick head gasket might be somewhat effective in allowing a gradient across the head-block interface, maybe 10 degrees or so?
The hottest area is the exhaust manifold, so reducing the surface temps of that by a thermal barrier coating to reduce its radiative heat transfer to the surroundings makes sense. Assuming a non-crossflow head, the situation with the intake manifold is different. The intake is bolted to the head, and after the engine is up to operating temps the head is going to be a fairly constant temp except for local hotspots in the combustion chamber and exhaust port. Hence, since the head and the intake are good conductors and they are bolted together then the intake is probably going to be more or less the same temp as the head, which will likely have a bulk temperature somewhere between your water temp and your oil temp.
I think it's likely that the best thing to do with the intake is to coat it on the exterior with a heat-dissipative (high emissivity) coating to try to reject as much heat as possible via radiation. The downside is that unless you spend DOD- or NASA-type money on the coating, it might be a wash because many high emissivity coatings tend to also be high absorptivity as well, which would tend to absorb more heat from the exhaust manifold. (see discussion of A vs E below...)
Surface finish and coatings can have a huge effect on the emissivity of a surface. Polished metal is pretty bad at radiating, so one possibility for the header rather than coating is to use a stainless header and shine it up real nice.
For the intake, rough surfaces radiate better so if you accept the philosophy of trying to radiate heat out of the intake, then an as-cast surface or a glass beaded surface combined with a light coat of flat black paint (remember we are trying to get it to be a blackbody radiator) would be the best solution short of an expensive aerospace high-emissivity coating. You definitely don't want to use a header coating that has low emissivity.
Coatings (including paint) can be categorized in their radiative thermal properties by stating the absorptivity (or A) and their emissivity (or E). A and E are dimensionless parameters bet ween 0 and 1. The ratio of A/E tells you whether the coating preferentially absorbs or radiates heat. Keep in mind that the actual amount of heat transfer is dependent on the temperatures of the objects that the coated surface can "see".
Someone mentioned not painting a valve cover so it would radiate better? Why would you want your valve cover to be a radiator anyway? But anyway, if you do, then the same suggestion as I mentioned for the intake manifold is what you want.
So the hot intake manifold is heating the cooler ambient air flowing through the intake manifold. So my thought was to keep the intake manifold cooler, it shouldn't absorb heat from the engine bay. If the radiant heat could be 100% reflected by the intake manifold, it would always be at ambient air temperature, except for the conduction effects from where the intake manifold contacts the head. (And I've seen some power gasket products sold for turbo manifolds to supposedly address this to increase power.)