“Why do judges have all this power to over turn the President’s authority?”
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Answer: They don’t. At least not constitutionally. The Judicial Branch can issue rulings until they turn blue in the face but they have no ability to enforce them. Enforcement is the purview of the Executive Branch. If the Executive Branch decides that a court ruling is illegal or unconstitutional then it can and should ignore the ruling. If the Legislative Branch doesn’t agree with the decisions of either of the other two branches then it can pass clarifying legislation. Of course, if the Executive Branch honors bad Judicial rulings then they’ve effectively surrendered their power to the courts. That’s what happens far too often.
In President Andrew Jackson's time, yes that was the case. Not now. Jackson had the power to fire any executive branch employee who failed to carry out Jackson's orders. With civil service laws in place, the bureaucrats can say "Sorry, have to follow court orders", and ignore Trump's orders.