What is your question? It appears to me that you are just making a statement.

What would cause this. Half the coils on the output side of the transformer burned?

>>>>>>Threads Merged<<<<<

Okay, this makes sense now.

Simple transformer failure could be the culprit. Do you happen to have a schematic of the circuit handy?

What I would do is verify that the components feeding into the transformer are providing the required outputs and if they are, replace the transformer and then search downstream of the transformer for a shorted component.

I would most likely use my Oscilloscope for this type of work, but you could probably do just as well with a multimeter.

One other thought, make sure that any fuse or fusible link in the circuit from or to the transformer did not open.

Remove load from output, measure voltage to input, then measure voltage on output.
What is the input voltage supposed to be?