I remember the transmission from another thread, I think. I'm still just as puzzled as you as to why the version number in the stock tune has to change.
But unless this is a totally new calibration, you SHOULD be able to operate your truck on canned tunes while you're waiting for your custom tunes to be rebuilt. (And, it won't cause any problem with your custom tunes either.)
Just start Pegasus, connect the Gryphon and click on [Update]->[Gryphon Update Manager]. Allow Pegasus to update BOTH your firmware and your calibrations (the tunes). Then, you SHOULD be able to reprogram your truck above "stock", and I would recommend the Level 2 "tow" tune as a very good all-around tune.
You should also update your registration in Pegasus with the new hex code. This MAY need to be done before you update the Gryphon itself, and I think it's automatic with the Gryphon plugged in if you click on [Help]->[Registration], then possibly [Clear] to remove the old data and [Retrieve] to transfer the new data.
Hope all this helps and I hope Bill is able to remake your custom tunes soon.
- Jack