Are Wages (box 1), Social Security Wages (box 3), and Medicare Wages (box 5) generally the same number when completing a W2?

In most of the cases, yes. If a employee has income more than $97,500, then the box 3 income is $97,000 and box 1 and 5 income will be more than $97,500.

There can also be adjustments for 401K contributions and Flexible Spending Account withholdings in the Box #1 figure.