Did you need to do anything extra for cooling? One thing that impressed me about old hardware that I did not appreciate back then is that the CPUs don't even need heatsinks. I imagine this PCjr don't have one either, but it's probably got a fan somewhere to circulate air through?
There is a fan internally in the machine, but it was placed to cool the 5.25" floppy drive when it was in use.
I have more open space in this machine because I am using a 3.5" drive instead. I also replaced the original fan with a quieter Noctua. The jrIDE is running naked on the side of the machine because I think it was having heat issues.
In a later iteration of this machine it will get more direct cooling; the slots in the case are kind of restrictive.