Among text lines is not an issue. You can embed SVG as regular images and even specify the height as e.g. 1 em.
The fact that it are thousand of equations can be hard. However, you already say that you have a Word document. With my add-in you can export the equations in the MathML format. From there it is easy to convert to SVG. For example with
http://www.grigoriev.ru/svgmath/. If you keep the name equal with the PNG images that Word normally uses, you should be able to use some smart Search/Replace rules to do a quick replace.