Every once in awhile (and by in awhile, several year span), there's a mist (like vapor) if you will coming from all my vents. Then there's a strong, strong metallic smell that literally within 30 seconds to a minute makes me sick to the point where I feel like getting sick and have to roll down the windows.

Yes each time this has occurred it has been with the AC on, but even after I turn it off it still continues to emit the vapor mist or whatever. The engine has been completely rebuilt (bought the car total and rebuilt it). We even have to replace the wiring harness (and yes it is the correct harness for the car).

What could be causing this and would it be harmful to my car long term?

I have an '06 Scion XB.

 

The car might have been rebuilt, but they ussually overlook the AC part when they rebuild it (unnesesary But ye sounds like it is your AC compressor, 1st try recharging your ac with R134a, get a can with the gauge and see what you are reading (should be within the green) if low recharge it, if full (closer to yellow), replace your ac compressor which will cost a bit.
Cheap solution keep rolling with windows down and do not use the AC

 

First guess is that it is leaking R134a from your A/C system. The system might be getting overpressured and venting and the vented freon is being sucked through the intake for the climate control. The metallic smell is probably the oil in the freon.

Have someone give the a/c system a thorough checkover.

 

Is the drain for the AC in the passenger cabin working? If the water doesn't drain from the AC you'll get periodic vapor venting, which could smell. It usually happens when you turn. Sometimes it dumps chilled water on your accelerator foot. Might be worth a check before you tap into the refrigerant.
I think the drain is in the passenger footwell on the driver's side. If you run a soft wire of some kind up it gently, or use air pressure, it will clear. One check is to see if you have water dripping from beneath the car when you run the AC. If not, the drain could be blocked.
MD

 

behind your glove box, you'll see a white door with tabs on the end, that is your cabin air filter, change it out and it may help the smell a little bit.