Let's not forget that Granger can fall in a barrel of shit and come up smelling like a rose. He lands on his feet better than a cat. You're right that the letters might be misdirection. But who's pulling these strings? Spencer is obviously involved. Unwilling to help Jackson, wanting him transferred, putting Conway on his ship at the last minute, then sending Granger/Jackson to where Maidstone, if successful, could out rank Granger and get his hands on Jackson. And perhaps, Granger.
Lets not forget that Granger has been told by a few very important people his homecoming would be special. One of which was the king himself I believe. The others, Cavendish and the Duke of Clarence. So what awaits him? Mark is a master of misdirection.