How do we guarantee the accuracy and validity of Buddhist scriptures?
I think you are forgetting that those world systems, mythology about the creation and evolution of man, gods, Brahma, etc. were all 100% real to the people of the Buddha's time based on what information they had.  If it makes it easier for you, feel free to reimagine them with the scientific terminology of today.  My expectation, however, is that in 2,500 years, all of those cutting edge theories are going to seem at little quaint, dated, and mostly likely wildly, wildly wrong.

What doesn't change, however, are the core principles of liberation.  These are not dependent on any creation story (as the truths of, say, Christianity are) but are instead derived from direct insight into how suffering is caused by craving.  While you are unlikely to meet any Nagas anytime soon, you are guaranteed to find yourself facing down all of the obstacles to liberation mentioned in the suttas.  The means given for overcoming them will also remain valid so long as there are humans able to hear them.