Hi and welcome
For about a year and a half I practiced this combination of AYP and ashtanga vinyasa, although it was in combination with full ayp routine (twice a day).
From the point of view of steady progress and purification of the nervous system, it would be ideal to do two deep meditation sittings twice a day, every day. From this point of view it's also better to favor your deep meditation practice over extensive asana practice of ashtanga vinyasa. After quite some time of practicing these two together, I've had to ease up on my asana practice considerably, because in combination with full ayp routine, it was energetically too intense (non-attachment to practice, huh?). Over time it's important that your practice is stable. This means cultivating our two sides - inner silence and ecstatic conductivity/energy - equally and in harmony. When you practice ashtanga vinyasa it causes purification of the body and nervous system and it mainly cultivates the energetic aspect of ourselves. As a standalone practice, it may lead to various energetic problems and maybe a kundalini awakening. But if not combined with meditation (like ayp) progress is likely to be unstable and it may be a "bumpy ride"
When you work intensively on the energy side (by ashtanga vinyasa), meditation can turn out to be pretty intense, because your nervous system is more open, more loosened up, so more obstructions are coming out and this causes the bad feelings. If you're aming for balance in your practice, it is important to self-pace. This includes self-pacing not only meditation but also your asana practice.
Regarding the sequence of meditation and intensive ashtanga vinyasa practice. In ayp it's recommended to wait some time and calm down a bit before doing your sitting practice. However, if it works for you without this pause, no one can say anything
It's up to you. Personally, I've found that it's better to calm down before sitting or I'd do the vinyasa sequence afterwards. It's up to you and what suits you best.
The breathing in ashtanga vinyasa doesn't really replace spinal breathing. But whether or not you do spinal breathing is up to you. It's most important to be stable in twice daily meditation, without needing to stop it because of overdoing with asanas. Self-pacing again
After you've been stable for some time, you can consider adding a new practice like spinal breathing. Remember that this intensifies energetic purification and it's necessary to not overdo in cultivating neither inner silence, nor ecstatic conductivity. Balance is the key.
Take care
