I am unacquainted with that particular set and so am unaware of the exact chassis used, however as you seem to have been ambitious to the extent of even trying changing the line transformer I wondered if you checked the IC circuitry associated with the vertical output? as JVC TV's of that era are notorious for faults developing in and around this circuit, the infamous C926 being a main player as the cause in many instances plus the vertical output IC suffering from bad joints, or indeed failing altogether on heat up.
Dependant of chassis the vertical IC can either be a TA8432K marked on board as IC421, or its a LA7832 and marked on board as either IC412 or IC1421
Another cap to look for is a C424.
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