A few corrections:
Assuming Henry's child by Jane Seymour is a girl then that child remains his only legitimate child - it is probable that her main influences would remain the Protestant Archbishop Crammer and her Seymour uncles - therefore she is a devout protestant.
At Henry's death there will be a serious problem if the younger daughter succeeds over two elder ones (both of whom whilst declared illegitimate were born legitimate). Under these circumstances it is highly unlikely that Henry would restore Mary and Elizabeth to the succession in the 1540's despite a concern that if Jane's line failed his direct descendants through either Mary or Elizabeth would be excluded.
He would have to balance the risks - its unlikely though that having failed to give him a son his veneration of jane seymour would exist in our time line so he might name Mary, then Elizabeth then Jane in his will saying nothing about their legitimacy or lack of it.
Mary's problem would remain that all her heirs with the exception of her cousins Mary of Scots and Margaret Douglas were devout Protestants.
Assuming the succession laws of the 1540's are enacted in TTL as they were in OTL then -
Mary was initially restored to the succession followed in the final act and will by Elizabeth neither were restored to legitimacy. Under the succession law and will Henry was followed firstly by his son, then any children of Henry and Catherine Parr and then the Lady Mary and the Lady Elizabeth.
In our scenario that is likely to read as
Any son by Catherine Parr, Princess Jane and then any daughters by Catherine Parr and then the Lady Mary and Lady Elizabeth.
There is no contemporary evidence that Henry suffered from Syphilis and actually all three of his surviving children enjoyed relatively good health in their infancy - Mary and Elizabeth both appear to have suffered heatlh problems when a in personal danger and b when they were particularly distressed or frightened. Edward was cossetted as a young prince but until his final illness was pretty robust. Henry's poor health in his last decade is mainly down to lack of exercise and a very unhealthy diet - as a fit and active young man his heavy and rich diet had been reasonable after his bad fall and his subsequent leg problems he continued to eat as before compounding his problems by gaining weight.
A list of the tudor succession in the 1540's was inaccurate
Edward (Jane in our scenario)
Mary Tudor
Elizabeth Tudor
and then by strict primogeniture
Mary Stuart Queen of Scots
Lady Margaret Douglas (niece of Henry VIII, half sister to James V of Scotland, Countess of Lennox and was born in England)
her son
Lord Henry Stuart Lord Darnley (b1545) (his mother later bore a second son Charles Stuart)
Lady Frances Brandon Grey Duchess of Suffolk (the King's appointed heir after his children)
her daughters
Lady Jane Grey
Lady Catherine Grey
Lady Mary Grey
Eleanor Brandon Clifford Countess of Cumberland (died nine months after Henry VIII)
her daughter
Lady Margaret Clifford