I have a that runs parallel with the front valve cover (with a nipple on it) from the water pump, under the brace, to the right, through the throttle body and into hoses which go into the firewall (for the heater core) Is it common to have two lines coming from the nipple on the metal tube?

 

That is the heater pipe on a 3400. The nipple on the top is not a nipple, it's a bleed screw.

Outside of going from the water pump to the rubber heater hose, the only other connections I know about are two small hoses to flow coolant into and out of the throttle body.

I can't see your attached pic on my phone. When I can check from my PC I'll let you know, but this does not sound typical.