Assuming that you are comfotable and properly fit for riding outside at similar distances and times:
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My first recommendation is to add motion to your trainer setup. You can go all the way to a Rocker Plate, or even make simple version with foam pads.
- Essentially, a rigid trainer and bike setup is unnatural. We move all the time on the bike outside and it rarely stays perfectly vertical, despite what we might think.
- Those slight changes in angle (even a degree or two) come from lane changes, pedals stroke motion and cornering. Each one of those variations is a relief to our sit structure and soft tissue.
- Adding even mild motion from some rocker or foam padding gives the trainer some movement that is otherwise lacking.
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Try to incorporate a standing break routine if possible. It does mean breaking from the aero position, but this can help extend comfort and time in the saddle. I find this a bit easier and more natural with the addition of motion from #1 above. But either way, getting up for even 10-30 pedal strokes in a 2, 5, 10 minute pattern can really help. Experiment and find a timing that works for your intervals and preference.