CAB 2000.1 Protection Flashing

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What would be the best way to test this? I have less than ohm across the 3 solder points for the secondary winding on the back of the board pictured earlier. I do not have an inductance tester. i did try to manipulate the transformer while powered up and did not get any change.
 
With thesmall wires attached to board going to lifted secondary windings it flashes in and out protect (LED's are flasimg red then green...)

With the secondary windings lifted the FETS are making a good square waves but no LED comes on ( red nor green are illuminating). I do not believe it is powering completely up when I have the secondary windings lifted.
 
I am using a 12 volt battery with an inline fuse the battery rests at 12.65 volts. I hooked up another amp today and it functions with no issues. When I first opened this amp up the power input solder wasn't great (maybe got hot or poor from factory) so I refreshed that and I am getting good voltage to pin 2 on all PS FET pads.
 
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