How to open 2 Adobe Reader instances?

Just go to the upper menu and click "Window">"New Window".

Then you'll have two instances of one document opened in separate windows.

You could make a (temporary) copy of the PDF in question, with a different name, and then open them both in Adobe Reader.

In Reader 20145.010.20060 you can simple drag and drop from the tab in the Reader window and another window will appear