Presumably if an isolation transformer was part of the OEM spec, then replacing it with any suitably rated and approved modern isolation transformer would simply constitute a repair not a modification and the unit would then be as safe as intended and any potential legal complications avoided.
The issue of any further mods for your own use is entirely up to yourself but it would be prudent to put everything back to standard if the unit were passed on to anyone else to avoid problems if they subsequently passed on as a result of using it