This problem has several aspects.
First, let's take the physical aspect. You write that you pray in the butterfly pose. The butterfly pose is such a rather difficult position if done correctly. It is quite difficult to sit in it and you should not sit on the hard floor in it, you need to lay something soft. The butterfly pose is a sharp stretch, and this stretch is most likely exorbitant, too strong for you, so your legs start to hurt.
Therefore, it is more expedient to put wooden or foam bricks (there are such in Iyengar yoga) so that the legs are comfortable. And only then, over time, slowly increase this stretch. It's good that there's a surge of inspiration. Oleg Gennadievich advises that you need to sit still no more than 45 minutes.
I do not advise you to wait for several flushes of dizziness and inspiration. We sat for 40-50 minutes and change position. You can also try other poses. You can pray while standing. You can pray in the diamond pose, you can on your knees. Try these poses, perhaps they will be more comfortable for you, you can alternate them.
By the way, a very important question is whether your joints hurt at all. If you have problems with joints, muscles, then these static exercises, these poses during prayer, must be combined with dynamics. That is, during the day do some kind of dynamic exercises. It can be Iyengar yoga or physiotherapy exercises.
From the point of view of the moral, spiritual aspect, When you pray, the most important thing at this time is not that your channels will be cleaned. This should not be the most important. The most important thing in prayer is to establish contact with holiness. And so, special attention should be paid to this. And the way the physical body feels, it should already be in the background. If you concentrate not on prayer, not on relationships with a holy person, but concentrate on the position of the body, on whether your channels have made your way or not, then this is not very good for prayer.
Channels will definitely break through if you practice spiritual practice. But when you set it to an end in itself, and you, apparently, so, what happens? Where we direct our attention, our false ego is directed there. In this case, you direct your attention to the physical body, to what happens to it, to the posture. You direct the false ego there, and it always brings suffering. It is his main function - to bring pain, and therefore there will be severe pain in the physical body.
It's better to put the question differently. When this pain begins, I do not think about whether my channels are broken or not, I give this pain to a holy person, I give it to the Lord as austerity in order to improve my spiritual life. And not so much to improve your spiritual life as to establish contact with holiness, with a holy man.
So far, you get such a slightly utilitarian approach that will not bring any benefit if you constantly think about how you sit. Focus your attention on the spiritual aspect.
One more thing: you write that you, unfortunately, do not pray every day. Prayer should be every day. It may not necessarily be 1.5 hours, but it must be every day. As every day we clean our body, develop it physically, so we must train our mind, we must wipe the mirror of our mind. I would even say that this is not just a mirror, it is a window through which we look at the world. And prayer just clears this window from karma, which comes every morning. Therefore, try to pray every day, at least a little, a little bit. Do not turn prayer into a physical exercise.
You write whether it is worth expecting discomfort in other parts of the body, whether this means that healing begins there. Pay attention to holiness. Recovery will take place according to the will of God as His gratitude, a beneficence for the fact that you still noticed that He is in the world, and begin to build some kind of relationship with Him. It will come as a blessing. Concentrate on the voice of the holy man. Try to serve Him, bow in your prayer.
I think everything will work out for you and wish you happiness.