would my aluminum (not conductive enough) tool box in the bed of my pick up work as an makeshift faraday box?

Aluminium is a good conductor (though not as good as copper) and a box made of this material will serve, to an extent, as a faraday cage.

The effectivness of the shielding depends largely on how well made the box is, and how closely the lid fits.

Additional protection may be obtained by placeing equipment in smaller metal boxes, within the larger box.

The most likely cause of an EMP event is the detonation of a nuclear weapon, and a well made metal box although not giving total protection, should protect against anything that the owner of the equipment can survive.

Unless the cage is well grounded to earth, the protection will be minimal. The box will serve as a resonant cavity, and will work better at some frequencies than others, but the higher the frequency, the less the protection.

I wonder if it would work in the bed of a pickup, since the pickup is not grounded to earth due to the rubber tires. Or would it be enough that the bed is "grounded" to the vehicle's battery? Looks like the battery would not stand a very large overcharge from an EMP.

It would depend on the voltage. With enough voltage (think lightning), the rubber tires ground the truck very well. In fact, assuming that you have a metal roof, cars act as faraday cages for keeping their occupants safe during a lightning strike, directing it around the outside of the body then through the tires into the ground.

Modern tires actually do conduct, they make them that way to cut down on the static electricity that builds up in the vehicle.