I am wondering if people who have already gone to heaven have a new, transfigured body right now. If so, does this new body they have now join with the resurrected body at the end of time when Jesus returns?
The bodies of the deceased remain dead, and for the most part decomposed (allowing for the incorrupt condition of the physical remains of many of the saints) until the general resurrection at the end of the world (the end of time/of the physical universe). Only at that time will the person’s body be reunited with the soul.
There no “substitute” body for those souls who are now in heaven awaiting the resurrection. However, a few exceptions to the rule of the general resurrection are to be noted, especially the virgin Mary, who by authority of the dogma of the Assumption is acknowledged to be, body and soul, in heaven right now. Others, considered by many of the faithful to be probably (although not defined by doctrine) body and soul in heaven are the prophet Elijah, who ascended to heaven in a whirlwind via a fiery chariot (2 Kings 2) and Enoch, of whom scripture says simply that “God took him” (Genesis 5:24). The body of Jesus, of course, is also reunited with his soul and divinity in heaven.