Additionally, in the original crack, i could put in an 12AT7 tube - and it would sound great - in fact, i found it to sound the best.
No. It will distort significantly and cause the 3K loading resistors to run too hot. It will also dramatically decrease the operating voltage available for the 6080. Just because it sounds different doesn't mean it sounds better.
But after i installed the small board of the speedball - putting in 12AU7 sounds very good but swapping it with 12AT7 make the sound distort.
The 12AT7 is not to be used in the Crack. There is absolutely no surprise here.
The 12AT7 is a fine tube and we use it as a driver in our Stereomour. It has too much gain to be used in the Crack (in the stock circuit with the 22.1K plate loads, there won't be as much gain but this sub-optimal loading will lead to a very euphonic and overly warm sound).
If you want to try a 12AT7 in the Crack, try 80K plate loading resistors in place of the 22.1K resistors.
If you want to try a 12AT7 in the Crack with the Speedball, replace the R1 resistors with 1K resistors.
This is the wrong tube for the amp, but if you want to actually hear it working properly this is what I would recommend.