mixing past and present sentences

Your tenses are fine, but there are some needed comma repairs.

You need the commas in this compound sentence with an introductory clause beginning the second sentence.

 a) I had headache, and, after watching the movie, I'm feeling good.

You need a comma after the introductory clause. Compare with a).

b) I had headache. After watching the movie, I'm feeling good.

This is fine.

c) The program that I sent you does not work anymore

You need a comma in this compound sentence.

d) I charged the phone yesterday, and it's working now