Affiliation on the papers extracted from the thesis I graduated from PhD almost 2 years ago and I am a full time assistant professor in another country.

A paper of mine was accepted recently (main paper of the thesis). 

1- Now my supervisor asks me to use my old affiliation (i.e. the university I studied) because she thinks I have completed the thesis while I was there. I received financial help for my PhD which I have acknowledged in the paper. I responded that I am legally bound to my new university and I could not do that. Am I supposed to do that?

Btw. both my supervisors are included as co-authors (with their affiliation which matches my old university).

2- Now again she asks me to at least put my old university's name first. I am the main author (and honestly have done all of the work. My two supervisors read my work, gave comments and possibly corrected English mistakes).

If I am the main author, the correct format requires me to mention my own university first. If I just change the order of affiliations list (a. old university, b. my university) and still keep my name as first author (my name *b), is that acceptable?

3- What is your suggestion for the remaining papers that come out of the thesis?
Your advisor is correct that papers published as a result of your thesis work should include the institution at which the thesis was done as at least one of the affiliations. 

The role of your present institution depends on whether or not you did substantial work on the paper there. If so, then you need to include that as an affiliation as well; if not, then it should be listed as a "Present Address."

What you cannot do is list just your new affiliation, with no recognition of your graduate institution.