With no engine in the car, I would move those front jack stands to the trans crossmember sub frame. To help the front of the car droop down into alignment.
Those cars flex all over the place when jacking them up.
First clue right now with the way you have it, do the doors hang low when you try to close them? If so, moving the jack stands to the crossmember sub frame will help to pick up the rear doors so they close better > body in alignment.
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