After death, do souls wait for the Second Coming to receive their glorified bodies?

Yes. A human being is body and spirit, and the spirit is sometimes called the soul. When you die, your body goes to the grave and, after the particular judgment, your soul goes immediately to purgatory, heaven or hell. The souls in heaven have a real, conscious existence, as Apocalypse 20:4 shows John seeing the souls of the beheaded who lived and reigned with Christ a thousand years, that symbolic thousand years being the time from Christ's first coming to his second. They simply do not yet have their bodies. When Jesus comes back, he first raises the dead, both Christian and non-Christian; the Christians' bodies are glorified in an instant and reunited with their souls, and then those still living are raptured up into the air, all of it happening in the air, at the Second Coming, not in a secret rapture beforehand.