GJgo,
Are you experiencing a hot running chassis? Is the power transformer hot enough to burn you? I will try to borrow a thermal probe from work to see how hot mine is getting but at the moment it remains just warm and does not seem to be a concern of mine. With the face plate removed, that will change the air flow characteristic of the fan. Since it is mounted at an angle to circulate air within an envelope, some outside air is pulled in as some is pushed out since it is a closed end box with one side open. Removal of the face plate will limit how much air passes out and one side may get hotter than the other. One would hope that air flow modeling was performed in the design of the chassis and enclosure to ensure good air flow around the tubes. Unfortunately, it is just a small box fan that can recirculate air from exhaust back to inlet as there is no air baffle to prevent back feed. When I run my JP-2C, I can go for several hours as it is hard to stop. I have yet to experience the super heated chassis like I have with the Mark V. I also have a RA100 (actually two). The head version had a rear cover that basically reduces the opening considerably on the back side of the amp. The small 2 speed fan basically pushes air over the power soak resistor but also helps keep the rest of the amp cool. However, I have removed the rear cover while I was tube rolling and noticed a difference as it seemed the amp got hotter with the cover removed, also the metal grill effected how the air flow passed within the cavity. Yeah, this one has a top grill too but I had better thermal performance with the amp with cover in place. Combo's can be excluded unless the speaker is sealed (Roadster combo) as they move more air than the fan (this applies to the Mark III and Mark IV combos).
If you are having heat issues, you have two options, contact Mesa Customer service and report the issue, and secondly, replace your power tubes as you may have one that is not matched or is out of tolerance. One way to find out what may be causing it, turn the amp around facing away from you, remove the grill and turn the lights out and play. If you notice the seams on the plates of the tubes turning cherry red but the rest of the plates are dark there could be something out of its performance spec within the amp or it could be the tubes themselves. Note that if you are pushing the envelope (high volume) it is possible to get the tubes to glow slightly (this is my experience with the simul-class circuit : Mark IV, and Mark V). I have yet to experience this with a Class A/B circuit as all the tubes are running at the same bias. The chassis will get warm but should remain below 180F (assumed, based on UL requirements for exposed metal parts that can be touched by hands, also this was the thermal limit for operating temperatures of electronic products that I have personally worked on in design and development). Also note that the chassis does not seal at the top of the shell in front, along the sides and on the rear as it does have an air gap to allow for heat dissipation.
What is your speaker load? That may also play a role in operating temperature....always best to match load to output. At least you have 3 options with the JP-2C. 16, 8, 4.