Just out of curiosity, why would you change the factory stereo out? I find
mine to be excellent  except the AM reception is poor. It is ok but just
barely.

The wiring harness has nothing to do with your antenna connections.  I
looked at the complete pin out on the Hyundai HMASERVICE website and the
coaxial connection is the only connection that feeds to the antenna.  If
there is an external antenna amplifier, it is powered from a totally
different source than from the radio.

the after market receiver is usually grounded to
the car chassis. when you hook it to the vehicle
antenna this provides a second ground, creating
what we refer to as a "ground loop".
disconnecting the second ground from the
vehicle harness (leaving only the chassis ground)
usually solves the AM reception problems.
Believe it or not this method usually works and
has cured AM reception problems on many
different vehicles.
Another bizarre AM reception cure is to install
a long coil of wire between the antenna and the
radio receiver. Yes the wire can be rolled up
on a spool and should be about 200 feet or more long.
this is insulated wire and could be coax (shielded).
I prefer coax because there will be less noise in the
AM signal.
connect the coax shield to chassis ground at the antenna
end, but not at the receiver end. The reason this works is
that AM waves are long wave, and using a short antenna
or antenna lead stops the waves from propagation.
You can use a very small gauge coax wire, does not
need to be a giant roll of wire. But the longer the wire,
the better your AM reception will become.
This works on home receivers too.
--advice from AM radio engineer

I know you are scratching your head at this, but try it
you could be amazed.