So if someone hypothetically had an alcohol distiller, would using say 90% ethanol be good for extracting syrian rue? or would the acetic acid and salt method produce a cleaner product?
What do people think about distilling the vinegar solution?

you have the right idea
an acidic alkaloid extraction can extract a cleaner product

though distilling an acid would require more energy. just do a good ol' A/B(/A , if storing).