I have been helping on the Downing family trees and share your frustration with the antecedents of Jane Clotworthy. I do not have a verifiable source for her marriage to Henry Downing on 2 June 1665. There is a portrait of 'Jane Downing' at Downing College Cambridge, which suggests that she was born in c. 1640. She undoubtedly married Henry Downing in England and I have no evidence that she went to Ireland except late in life after Henry's death to live with her son, Colonel Adam Downing, who by then held estates near Bellaghy. She does not seem to be buried at the Downing Mausoleum at St. Tida's, Bellaghy. I have seen a family record that suggests that she was the daughter of Sir John Clotworthy, 1st Viscount Massereene and his wife Margaret Jones, but she does not appear on Clotworthy pedigrees. The 1st Viscount was b. c. 1600 so it is biologically possible, but he lived mainly in Ireland. He did return to England to become a member of Parliament and was involved in the impeachment of Thomas Wentworth, Earl of Strafford, in 1641. We know that he had a daughter Mary, who married Sir John Skeffington, and Skeffington became the 2nd Viscount Massereene, but there is no record of a second daughter. A second issue is that Massereene was strongly Puritan and the portrait is of a rather decolte lady in the style of Sir Peter Lely (perhaps painted in c. 1665, after her father's death).
I have done a lot of research on the Downing family much of which is well documented and researched (mainly by others). I would be pleased to learn if you solve the problem. Robert