How and where did the scientific method replace fantasies and suppositions about the universe?

The scientific method probably replaced fantasies and suppositions about the universe during the Age of Enlightenment that preceded the Renaissance. Leonardo Da Vinci is perhaps the best example of the rational application of the scientific method in the Renaissance.

Is the idea that the universe is infinite and never-ending a religious idea or a physics equation?

The idea that the universe is infinite and never-ending is both a religious idea and a physics equation.

Whtat is Occam's Razor and how is it used in physics?

Occam's Razor is the principle that only observable facts should be used to find the simplest possible explanation for scientific theories.This could be paraphrased that simpler is always better and it is more likely to contain the truth.

If the universe is 85 percent dark matter, why was it only recently discovered?