Now that I’m beginning to train more specifically on the TT rig I’m finding that efforts/intervals are harder in the TT position than road bike. Do you have any recommendations for moving across bikes. Two FTP.’s? Train off the lower one/higher one?
This is similar to what we see when people transition to riding indoors to outdoors, their power is usually lower inside on the trainer. My suggestion is to keep riding the TT bike so you can get more comfortable with it and use your HR and perceived exertion as your guide (along with power). If it is still a significant difference, you could do another FTP test (or use NP data from a hard group ride).
Also do your yoga and work on your hamstring flexibility and hip mobility - will allow you to decrease your trunk-torso angle (bend down in the TT position) and still be able to make watts.
Don’t forget your REVO exercises too to get some watts out of your glutes