What sort of custom intake are you doing? PVC pipe going into the throttle body?
Someone did a battery relo here, except they moved it over to the driver's side where the washer fluid tank is. Was it Ray Lobato? Anyway, I have thought about it myself. Your idea about putting the custom air intake up where the batt is now seems to be a good idea. Almost every single filter car made has it's air filter as far forward as possible, I assume because it's furthest from the engine heat.
I have taken underhood air temp measurements and found that up where the batt is, behind the pass headlight, temps were about 125 degF on a day where outside air temp was 85 degF.
Back where our stock airbox is, at the back where the vac tube hooks into the airbox, the underhood air was 145 degF on the same 85 deg ambient day.
I think 20degF makes a difference. Also, if the air filter is in front, not only are you getting cooler air in, but it also makes it MUCH easier to do a custom cool air induction mod. I.e. you could easily run the insulated dryer hose just a few inches and with few bends to a spot in the front.