Nothing a real hose clamp can't take care of! Seriously, just route it through the top - when you get your aluminum that is.
I don't use that box crap on my car, just use your existing wiring. I gave mine to Rinku b/c his 1st thermo box failed him. I think that's common with the FAL boxes.
Jesse
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Ings RSpec, Built KA24DET, GT3071R
VR-4 AWD/TT Winter Sled