Re: Richard Clarke
Thomas Clarke of Plymouth may not have been the son of the Master's Mate John Clarke who helped bring the Mayflower' special cargo to America. As you said, Clarke died in Virginia. He died after arriving in Viginia aboard the Providence, a ship under Captain Daniel Gookins, presumably after contracting a disease brought to Virginia at the same time by another ship, the Abigail. This disease killed hundreds of settlers shortly after the Indian Massacre, so the colony was decimated by two disasters in a row.
In response to John's death, and because of his long service to the Company and to his successful rescue from Spain where he was held captive for years, the London Company granted his widow special patents to land in Virginia. Her sons could only have redeemed the patents back in Jamestown settlements, where the Company had authority.
One son, William, had actually been aboard the same ship John was on when he died. This William received patents probably first in Elizabeth city, but he and his brother John later settled in Henrico Co. That is where many of Master's Mate John's early associates ended up settling.
Most of Clarke's children were baptised in St. James Clerkenwell's parish records. It is possible that Thomas, christened in St Dunstan Stepney parish was his son, but it hasn't been easy to prove. Nothing ties him in with John Clarke except for names on a baptism records.
Hope that helps out in someway. IF you have any questions or need any sources, just let me know.