Dear SR,
Basically, we need to be responsible guardian for the pets, as they love us more than we do.
So, be sure not to leave them alone or locked up in a room, when we meditate. Instead, we would feed them half an hour before our meditation starts, for they will develop a tendency to sleep, while we meditate.
We can be inside a mosquito net to meditate, so that the pets see us what we are doing. Gradually train them to co-operate with the scenario, as they are sure to learn from instincts (only instincts).
Now, for the feelings on body parts. Its a common feeling in everyone because meditation makes the body parts very sensitive. That makes us easily feel every small happening of the body. Gradually, with steadfast practices, we learn to forget the body and get used to the thoughts alone.
About the muscle pain, we may channelize this discomfort towards a particular chakra we are comfortable concentrating in.
Lying down for meditation is a good idea, provided the mediation does not last for more than half an hour, or else we may fall asleep.
Love
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