Is it safe to have a furnaces exhaust pipe facing to the side instead of down

It turns out the problem was that the zone valves were installed backwards. They closed in the opposite direction of the flow of water. Since the zone valves were fighting the flow of water, it was causing a great deal of vibration and banging.

I had the heating company come back and reverse the zone valves so they operate in the correct direction. The banging is completely gone.

Can you look at the furnace during the time it is blowing cold air and see if the flame is on?

The thermostat has the ability to control the fan, but typically the thermostat sends a "turn heat on" signal to the furnace and the furnace controls are setup to turn the flame on for a X amount of time (to warm up the air) and then turn on the fan once the timer expired (so the air coming out of the vents is not cold). When the heat is turned on is the flame and fan going on at the same time?

Not sure about your furnace, but some have a couple of LEDs that are lit up and can be used to read a status or error codes. If you have the manual you could try to decipher the code while the cold air is running and see if it gives you a clue.

I would start by trying to figure out if the problem is with the thermostat or the furnace by installing a new thermostat and seeing if the problem goes away. If the problem is still there you can just return it. I had a furnace issue where it was going off randomly and would work in heat mode but not cool mode. It turned out that the thermostat was bad and sending intermittent signals.