This is embarrassing. Through my own clumsiness and sticking a screw driver where it didn't belong, I wiped out the output devices on the right channel of my amp. Frank repaired it and generously ate half the cost himself. My dilemma is that my set has been sounding so off balance and I finally figured out what is happening. The right channel isn't broken in yet.
You are jumping to conclusions. Most so-called break-in problems are not really that. Whenever you have a change or failure, or rearrange anything in your system, you break up the harmonious flow of chi. Many times, the correct flow of chi takes hours or days to re-establish itself.
But, there are some obvious things to check:
Mpingo dot location/orientation: Many times, when the system has been assembled or disassembled, the location of the mpingo dots is disrupted and winds up slightly misplaced. Given that the wavelength of audio signals may be as little as .6", misplacements of even half that*1 can drastically affect the phase and damping of any standing waves WRT the centroid of the disk. Even worse, if you incorrectly orient the grain of the wood, it can end up having *absolutely no effect* on the sound! Not marking the direction, and not making jigs/fixtures necessary to correctly orient the Mpingo dots, is a classic rookie mistake. Note that this is closely related to the flow of chi mentioned above, so it may never be possible to objectively determine if the problem was incorrect dot placement, or simply a transient disruption.
Pyramidal enclosure orientation: If like many high-end audiophiles you are using a pyramidal enclosures and stands for best sound, recall that pyramids only channel the energy correctly when aligned with the faces along a north/south axis. Note also that, since you originally ran the amplifier last, the position of magnetic North has shifted slightly and that, and not a poorly-broken-it amplifer side, can disrupt that perfect sound.
Oxygen leaking into interconnects/speaker wires: We all understand the vagaries of oxygen-laden bad-sounding copper conductors. But when you short of otherwise fail only one side of a system (amplifier in your case) it's entirely possible that the oxygen diffusion rate was different on the interconnects or speaker wire during the time they were exposed to the air. Differences in the oxygen content of the copper from side to side can play havoc with the imaging. This is very hard to avoid with the typical 50's-style "hi-fi-den" listening rooms containing large amounts of free oxygen, which is what led many leading audiophiles to experiment with oxygen-free listening rooms. If you are on a budget, simply enclosing the active audio components in a vacuum chamber can have remarkable effects on the sound quality. A typical household mercury diffusion pump can evacuate down to 10^-4 or 10^-5 torr, which while far from ideal, can significantly improve the sound of the typical audio system. Note that this also allows vacuum tubes to function without the bad-sounding (and usually microphonic) glass envelopes, so you can have a secondary benefit.
Note also that in some cases the detrimental effects of oxygen diffusing into the conductors of interconnects and speaker wire can be halted or even reversed by the use of the various proprietary cable break-in tools. If your test equipment is not up to the task of measuring the effects, its best to contact the cable manufacturer for a recommendation. Power cables, once damaged by oxygen (or dark chi flow) cannot be effectively repaired and should be replaced.
Differential charge on power supply: if the battery bank for the right and left channels is not at the same state of charge, it's obvious that the correct channel balance may not be acheived. A simple audiophile-quality hydrometer reading of the battery acid pH can confirm this quickly and it's a simple fix. Note that although the typical navy-surplus submarine battery commonly used in mid-fi applications can run a typical system for some weeks or months, audiophile quality supplies need to be charged at least every 15 minutes. This should not be a severe hardship to the serious music fan, as most high-end source material (i.e. wax cylinders or 120 ips reel-to-reel tape) contains less than 2 minutes of content. Note also that there have been some recent experiments with the so-called "continuous battery chargers" consisting of an array transformers, diodes, and capacitors that supply the battery from common household AC, but until such technology is perfected, the wise hi-fi enthusiast will steer clear of these sorts of fads.
Hopefully these simple troubleshooting hints will locate the source of your problem. If not, then please post the details of your system (and any skin galvanometer readings you may take) and I'm sure we will be able to narrow it down for you.
Brett
* Nyquist's theorem, look it up