Allow me to express my opinion, but I think the whole idea of I/H/E engine modification is amiss. If you really think about it, I/H/E is actually the reverse order in which these mods have to be done. Thus it should be the other way around--E/H/I.

My reason behind this is that it is pointless and counterproductive to increase the intake capacity if the exhaust itself is restrictive--which it normally is if it is stock quiet, right? Afterall, what's the use of having a better, higher flowing, more efficient intake if the engine cannot expel the additional air and fuel out of the exhaust?

So if the car's exhaust is quiet(which it likely is, if it is stock and is in good condition), then the obvious system that needs to modded first is the exhaust. Only after the exhaust flow capacity has been increased will any improvements in the intake really take effect.

Now, as to the proper logical order of the modifications, if they are to be done on a step-by-step basis, I think the exhaust AFTER THE HEADERS/MANIFOLD should be taken care of first. This should be followed by the headers AND the porting, done together/simultaneously(smoothing of flow surfaces in the intake and exhaust ports), then finally the intake, which should be done last.

To recap, the order of the mods should be as follows:
1. Exhaust pipe AFTER the manifold(obviously includes the muffler, resonator, and everything in between the exhaust manifold and the tail pipe)
2. Headers AND head porting. The surfaces of the ports are smoothened and polished and matched with the headers and the intake manifold.
3. Replacement of standard air intake with Cold Air Intake or Ram Air Intake.