The output transformer may well be ok; did you isolate the transformer connections before making your measurements? If not then the results probably don't mean much.
Check out Tube Amplifier Debugging Page
My output or power transformer is dead, isn't it? How do I test it to find out?
Are you fitting slo-blo / 'T' rated fuses?
Is a suitable fuse fitted for the HT / B+ (eg not 10A)?