I just hope you can figure it out eventually. It's encouraging to know that the TF does work in front of the amp. Since the inter-stage connections in tube amps are usually, in essence, hi-pass filters, if there was a problem with lower-than-designed frequencies coming out of the TF, it would mask it, but… at least it's working and sounding good.
If/when you get around to testing this again, please either post or PM me if there's anything I can do to help, ok? I'd be more than happy to lend any assistance I can.