Agreed. I would look at valve clearances first (not since it's necessarily the most likely explanation, but it is by far the easiest to check and it's routine maintenance anyway so may as well regardless unless you know it has been done very recently), then second injector condition and cylinder compression since those two make sense to check at the same time, overlapping work to R&R the injectors.
On the other hand, if it runs pretty well otherwise, it might not be worth really worrying about this. Other explanations could also exist that would have no negative significance, like design differences between the 1-3 and 4-6 exhaust manifolds that let one of them shed heat to the air faster, differences in EGT probe placement, etc.
As for cooling the intake charge, can't see it helping in any real way if as you say it's already drawing cool air thanks to the airbox design. The big reason for the intercooler helping on a turbocharged engine is because the turbo itself adds a very large amount of heat to the charge air, both due to contact with hot machinery and also (mostly) due to basic physics of pressurization (see
Ideal Gas Law). By cooling that heated air back down between the turbo and the engine using an intercooler, it makes it denser (more oxygen, more power potential) and also helps control engine temps, giving dual benefits in that situation of a forced induction design. But since nothing is adding heat to the charge on a NA engine, you don't have to worry about any of that, as long as the engine has access to reasonably cool ambient air in plentiful supply.