This is my first try at contributing to a discussion, so I hope I get the jargon right.
As I see it you've got two issues, to turn Mary protestant, and then to ensure that her short reign is not just an aberration with history returning to its actual course. Since she seems to have minimised her exposure to C of E forms of worship by insisting on keeping the catholic rites, I suggest you have her undertake a study of the works of Luther and others. This is done with the intention of writing a defence of catholicism as her father had done before her - she was well educated - but against her will she is gradually persuaded by Luther's arguments. She still remains opposed to the C of E settlement, as that has made her illegitimate.
Then suppose that Prince Edward dies in infancy. Henry VIII, with no male heir, is obliged to recognise Mary as next in line, followed by Elizabeth. Mary comes to the throne in 1547, marries a British nobleman soon afterwards instead of Philip of Spain, and produces a male heir before her health deteriorates. He is raised as a protestant. When Mary dies in 1558 her young son is crowned, but has no effective power at first as he's still a minor - like Edward VI OTL. Cranmer is still Archbishop but is unlikely to live long beyond 1560. Casting around for a reformist successor, I found a possibility in John Hooper (Bishop of Gloucester under Edward in OTL).
I imagine the Spain-England conflict would pan out much as in OTL - there's still the basic catholic v protestant tension, and the lure of the Spanish Main to tempt men like Drake and Raleigh.
The issue of funding the government, and parliament seeking to exploit its hold of the purse strings, is still going to come to a head sooner or later. Perhaps however under a more puritan monarchy, it would be the anglo-catholic nobility that rebel and the Commons that sides with the king.
Union with Scotland could be helped or hindered. There's no united monarchy unless Mary's line fails, but a puritan England and presbyterian Scotland might find affinity sooner.
I think the most interesting effect might be in America. What if England becomes the refuge of choice for fringe groups like the Anabaptists, while the English anglo-catholics find things too hot for them and flee to form colonies? Could we eventually see an episcopalian USA, where the church is an integral part of the state instead of being constitutionally separated?
Anyway, there's some thoughts, to be expanded or shot down as appropriate.