I don't think the fender wells will really vent that much heat. Remember your tires are going to fling water and debris as you are driving. At least on the front it wouldn't be that bad, but something to think of.
Looking on eBay, that front fender liner is $42 new shipped (its aftermarket) maybe try it one side and see what happens to your temperatures as an experiment? I'd cut the aftermarket one and keep your OEM one though.
On the hood and rain guards, any thing that keeps water out will impede air flow.
I just finished installing the Trackspec hood vents to my car, which is a daily driver, and driven year round. I did go over the engine bay connectors and add dielectric grease to each one for extra insurance. However they are all weather tight connectors already. Your engine can get wet, its sealed it. The only way I see this being a problem is if you had a hot air intake where your air filters were exposed in the engine bay, as the side vents would most likely be very close to them. I know lot of factory cars have vented hoods, and I had several Mustangs that had aftermarket hoods now with scoops that were never a problem even when right over the distributor. Its just not a concern for me.
I'd say if you really don't like the look of the vents, I think you would be better off with one of the custom hoods, or the custom bumpers that have extra venting in them.