1-I thought with my self.
= I thought to myself (I think this is what you mean)
eg. "I thought to myself, 'Why does springtime always look so beautiful?'"
2-Does this natural in English to say.
= Is this natural to say in English?
= Does this sound/look natural in English? (sound for speech, look for writing)
3-I thank you to taking time to me.
= Thank you for your time
= Thank you for taking the time to help me