I have decided that my work investigating the inner mysteries of the TS-50 may help other people also, so from now on whatever interesting info I will find on the subject will be published here under a dedicated category.
A typical problem with the TS-50S is the internal -6.2V supply that is critical to the ALC circuit. This supply is one of the weak points of the TS-50 and needs to be checked in case of problems with the power output. It is also by design unable to operate unde approx. 11.5-11.7V, so if you run the TS-50S on a battery and have problems just replace R208 and R209 from the TX-RX UNIT (X57-4220-11) with 18K resistors instead of the 22K original ones. This way the -6.2V, the ALC circuit and the final output stage will work correctly down to 9.6V.
You have to thank VK1DL for this solution.