Actually you are right about parts but as Thomas didn't use in house IC's and all the divider pack and coupler circuits were available as schematics in the Service manuals available from ORGAN SERVICE CORP, ordering via the net. Some parts are available too, at a price though. Here in Australia a lot of the older organs are going to the tip so if you are in the right place at the right time then parts can be had.
Cross modulation distortion seems to be a problem with the amplifiers used in most of Thomas models, at this moment in time I am trying to sort this one out. Some held chords sound bloody awful in the upper registers, has any body else experienced this or is it just my ears. You experience something similar in Electron Tube organ amplifiers but not quite as bad.
I consider it great fun to refurbish these old organs but you have to know what you are doing (read electronic background) and have a lot of spare time at your disposal. With modern components you can even make them better than they were leaving the factory, in the Thomas case most definitely so. When I bought a Bel-Air mod 555 in 1970 new it had a fault delivered to me, no lower keyboard non flute stops. The fault is in the auto rhythm organ option If you can actually play, ( really don't see the point of a rhythm modulated lower keyboard ) just jumper the connection. Transistors used by Thomas were prone to failure, the good news is transistors today are very reliable and very cheap in 100 plus quantities. You can replace the lot, given the time. One other point is the inductors used in the tibia filters, these can go open circuit but it is possible to wind a replacement with a small pot core.