I doubt it is the tone stack if my assumptions are correct. I believe the tone stack components are shared between the clean channel and the Hi/Lo channel but the connections are managed through some small relays. I could be way off with the assumption. I could confirm this if I dared to remove the main preamp board and follow the traces from the tone controls of the Hi/Lo channel. I did pull the chassis of both RA100's so I could compare the two. It does appear there was some repair work done on the amp I am having issues with. Perhaps there was reason why the amp was up for sale in the first place.
I will see what I can do for repair. There seems to be a location that is 2 hours away but not sure if they are still certified as the list on Mesa's website is not always up to date. I was planning on using compressed air to clean off all debris on the circuit board but found that my air compressor was missing the regulator. It is possible it came loose as I found some of the parts on the floor near the compressor, but some parts are missing and not in the location they should be unless the frogs that have invaded my home have a taste for compressor parts. They are rather big in size and so are the spiders on occasion. I better stop while things are still okay as far as I know or something else will be not as it should be. I blame it on the Gremlins or perhaps the amplifier gnome that lives under my house who wants me to get the JP-2C instead. I did see the gnome on a few occasions. Here is a quick picture I took of him looking at my RA100 Combo when I got it.