In both #1 and #2, the verbs are virtually interchangeable. You can use 一緒に住む, or you can use 同居する, and both will be equally understood. In your example #3, I think there is a problem in that the two verbs are not identical. 進める means to proceed with something (some paperwork or some procedure), while 進行する means to advance or to make forward progress. Similar, but not interchangeable.
In any event, to answer your question, there will be no shortcut for memorizing which -suru verbs are interchangeable with their stem form. It is a case of exposure, repetition, memorization, experimentation, etc...