Good day all, I am unsure of this set up. Are there clearance issues with this type of system? It also draws it’s combustion air from the room it’s located in, they also have a desk set up in there for x-ray imaging. The room is approximately 4’x6’
Did You check the manufacturers recommendations?
James, if you have the make and model, you can Google the manufacturer’s installation instructions and that will, typically, give you what you need. 
The best to you.
Appears to be a NG high efficiency condensing furnace.
Intake is wrong. Requires an elbow to prevent accidental blockage.
Exhaust is likely wrong as well I suspect.
Look at the chimney clearance.
Look at the lack of counter flashing.
Definitely need a short piece of pipe and an elbow on the intake. Also if the room is only 4x6 it better have louvered doors or be bringing in fresh air from somewhere. Don’t personally see a problem with venting next to the chimney. I could not find anything about it in my bryant furnace install manual, which should be the same as tempstar as they are the same furnace.
It is nice to see you back after a couple of years, James.
Hope to see you more often… 
Unless it’s got a pretty high ceiling, it sounds like inadequate combustion air space.
Combustion appliances require 50 cubic feet per 1000 BTU per hour (BTU/h) aggregate input.
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