Hi Clodo. I understand you to say that both are version 1 (1st generation) model T's (without the mid select switch) with same components but they sound different. Have they both been thoroughly serviced with new filter and bias capacitors, potentiometers and jacks checked and cleaned, etc? Have new tubes been installed and biased and are they the same brand and type? Are you comparing them using the same settings, same speaker cabinet, same guitar and same ohm setting? In other words are you comparing apples to apples? If so and they still sound different keep the better one and send the other to me. I will waive my normal disposal fee and recycle it for you.
Perhaps one of them has been modified in the past or has a failing cap or resistor. Maybe a dirty jack. Weak transformer. Several things could add up so they really need to be checked out after you have covered all the simple things.
I just put new KT88's in a 1st gen, biased it and rebiased my 2nd gen (6550's) so I did some side by side comparison. I didn't get too crazy loud and they sounded very similar to my tin ear. Both very nice although some might say they are inclined to be rather rude if their knobs are twiddled.
Here's some amp porn.