I missed to include 1099-SA. As only the form 8889 is changed due to this, should just file the changed 8889 and form 1040x. Also should i file state return in this case?

You only need to file the federal amendment ... this is not a state issue.

@Critter#2 , Thanks for your response, that helps for the state return part, just to clarify the first part of the question, For Federal amendment in the above case, should I send all the Federal forms along with 1040x, or just the 1040x with form 8889 that was changed?

ONLY  what changed is sent ... so just the 8889 with the 1040X.