Is there a well-sourced, scholarly siddur/work on the siddur/website that discusses the origins of the various prayers? Where can I find it?
Eizur Eliyahu is very scholarly, it is technically a siddur according to the nusach of the Gr"a but attempts to get the text closest to what the Gr"a had. (possibly available Here)
Also Rav Ahron Lopiansky put a sidur together called Aliyos Eliyahu, featuring notes on the bottom that trace the sources of each tefillah and its Talmudic Source