Not necessarily. I think the common sailors are the ones who sided with Mary I during the 1558 crisis, though I'm not sure. It could be individual officers. Though your probably right. Any ideas as too which admirals would be pro-Jacobite?
Not really, though apart from Orford and Berkeley themselves, most of the captains would probably have been at least crypto-Jacobites. The Navy was more sympathetic to James than the Army. James had been Lord high Admiral before he was King, he was a good sailor, and well respected by sailor men . And the effects of James's proselytising were less marked at sea than on land. Also, the Navy had been fighting the Dutch for centuries, there was little love lost there. A few captains would follow Orford out of persona few would go over to James immediately, most would wait and see.
So Anne was a bit like Carlos II in that regard. It wouldn't be hard to bribe the doctors for the report beforehand. I'm glad it's not ASB because I really like that idea. Though with Anne you can never be sure what her real thoughts on James were. After all she is the one who persuaded Mary that James wasn't their brother, thus partially contributing to the Glorious revolution. Though in later life, I always got the feeling that she regretted what she did but could never admit it because that would mean admitting her own guilt. Though your right a deathbed reconciliation would be powerful propaganda.
Thanks

. It's a great idea.
So if he's in the Netherlands he's untouchable, for the most part. Again unless a servant can be persuaded to kill him but that sounds unlikely.
It would not be necessary to bribe the physicians (doctors then were lawyers or churchmen) . They were happy to provide the report, just the Council never asked for one until the Dukes took over.
Anne reportedly became very guilty about her treatment of her father and brother later in life.
So long as Stair _stays_ wherever he is, he's probably no problem. It's only if he tries to return
As for the other points you brought up, I would say the Catholicism would be a bigger problem then the Act of Settlement. I came up with an idea with that. After the reconciliation, Anne order's the act repealed (never mind that at that point she's in and out of consciousness, If only the conspiracy members see her its a moot point) thus when she dies James is immediately proclaimed King.
Problem is, that Anne can't (even in her senses) simply order the Act repealed. An Act of Parliament can only be repealed (or amended) by Parliament. I think that the Parliament of 1714 might have been willing to amend the Act, but these things take time. Weeks , at least, not days. And setting that in motion would be a dead give away.
The religion is a bigger problem, though again not impossible. Perhaps a law could be passed limiting a Catholic monarch's power over the Church of England? The only example I can think of would be Saxony. The Elector had converted to Catholicism to become King of the Polish-Lithuanian Commonwealth, and transferred authority over the Lutheran churches and schools to a government board. So a law could be passed by parliament doing something to that effect. Oh and a guarantee that his children would be raised protestant. Though I would assume that the Royal family would be more sympathetic to the Catholics and other religious dissenters.
But that would destroy the principle that the King is Head of the Church on Earth, an absolute fundamental point of the Church of England. I also think that if he were willing for his children to be raised Protestant, he would be willing to convert himself. It is useful to bear in mind, that apart from the issue of the Pope of Rome, there was not a lot of theological difference between the High Church (the supporters of indefeasible hereditary right and passive obedience, James's natural constituency) and the Roman church. It was the Pope that was objected to. A shrewder James might make use of that. Though, again, I cannot but think that a shrewder James would declare himself Protestant (even if he lied !) .
So that now We've pretty much planned out the conspiracy, any ideas, or books to recommend, about how James III would reign? I would guess he would be a very cautious about how he governs, especially on the first years of his reign. He would have to be more like his uncle Charles and (somewhat at least) his greatgrandfather James I, rather than James II and Charles I. I also wonder what would happen with the Act of Union? I mean on one hand the Stuart Heirs always use both the English and Scottish numbering and a large amount of their support came from Scotland (and a lesser extent Ireland) but on the other hand, the Kingdom of Great Britain seemed to be the dream of many Stuart Sovereigns.
Also any ideas as to a wife? I guess she would have to be protestant ,though I wonder if an Habsburg would be acceptable thanks to Britain's alliance with Austria? The ones I found are

rincess Charlotte Amalie of Denmark, Princess Ulrika Eleonora of Sweden, Archduchess Maria Josepha of Austria, and Infanta Francisca Josefa of Portugal.
I'm reluctant with Charlotte since she's only 8 in 1714 and with Ulrika Eleonora sense she's a bit old and the heiress to Sweden. IDK if Britain would want to rick being involved with Sweden and the Northern War. The only real problem I see with the Archduchess is her religion. Its the same with the Infanta, though she has another problem, in the sense that the last Infanta was barren and James would no doubt be reluctant to risk a barren marriage.
Also, I'm not sure if I want to have Louisa survive in 1712 or not, but if I decide to do so, any ideas as for a husband? Personally I like her for King Philip V but I know that it's unlikely. I'm not sure if a better spouse would be a King or sovereign or a low ranking Prince who could stay in England (similar to Prince George of Denmark and Anne), epically sense she's the heiress presumptive to the throne.
Finally I can't help but wonder how this would effect British politics long-term. In OTL the Glorious Revolution's bill of rights and Act of Settlement are what began the shift of power from the Crown to Parliament but with the act being thrown out and the Bill of rights possibly being edited (I would guess the parts about James II and any parts about Catholic succession) I wonder if the Crown would maintain its power and continue to use royal prerogative longer?
As to the nature of a reign of James III & VIII, it is hard to say. The OTL James would I think have made a stuff up of it, he was in the mould of James II & VII or Charles I , not James I & VI or Charles II. But, this is alternate history, and something must make it alternate, so we may perhaps assume that *James is a shrewder man, more like Charles II .
How would Charles II have managed things. Well, probably first, a Declaration of Pardon, like the Declaration of Breda. Then something to try to reassure the religious folk - " although my conscious doth forbid me to turn from the faith in which I was born and raised, yet knowing full well the love my people have for the Church of England, and I loving it kindly , for the love they bear it, and I them, I do vow by all that is holy that in all matters relating to religion I will be straitly guided and counselled by such goodly divines as my beloved Parliament shall propose etc etc ". Another Hampton Court conference, perhaps?
The Union was very unpopular in Scotland, (the Scotch Parliament was heavily bribed to pass it). A cunning man might repeal it, and then use Scotland as a foil to England.
I think that one place where a Jacobite Restoration would have enormous effect would be Ireland. In OTL, it was despised , not least because of its Roman Catholicism. That would be a plus for James. So we would probably see Ireland treated a lot more nicely, and having a lot more influence. Of course, that might well mean a civil war in Ireland, the Establishment wouldn't take it lying down.
Marriages, I'm not good at marriages. He must repeal the Act of Settlement , and being a Roman himself, he may as well marry another Roman Catholic. Perhaps a Habsburg Archduchess could bring a port in the Austrian Netherlands as her dowry ? (I've always wanted to see England get a foothold back on the Continent).
Louisa's marriage prospects, of course, improve immeasurably if her brother becomes King. From a nobody, a penniless refugee, she now becomes the sister of a King. And with a dowry , too. A very enticing morsel. But whoever she marries, even if only a minor prince, she would of course live at his court. The situation of the Prince of Denmark was anomalous, because Anne was in the direct line of succession. We know that James was fertile, so we can expect that there will be a *Bonny Prince Charlie to carry on the line, so Louisa becomes just another princess.
Long term politics, would be utterly different. Almost impossible to predict the extent of difference, but huge. James III & VIII would _rule_. Not just reign.
I doubt that even the Stuarts Restored could convince the English of the Divine Right of Kings. But passive obedience would certainly be loudly preached. It depends a little on whether James's succession is peacefully accepted , or if he has to fight for it. If he fights , and wins, he is sure (unless he is a fool) to greatly change the relationship of Parliament and King. To make it much more like the Continental models. Parliament proffers petitions, and registers the King's ordinances. And taxes are voted for life, at least. Whether he and his successors could do that without setting off another Revolution, is another matter. If he is peacefully accepted, then the opportunity to redefine matters is not there, and he will have to box clever, like Charles II . But, no matter what, he will _rule_.