Yep, you're on to it.
Kings Guard reported to Gold Stick. Main army reported to Captain-General or, later, Commander in-Chief. Guards were whatever regiments the King decided to honour with the appointment. There were different rules about commissions, promotions etc, Guards were an elite.
Unallocated lands in the Colonies (ie whatever the King hadn't granted to someone) were Crown estate , the King could do what he wanted with them. Bear in mind though, that most of them would have Indian inhabitants , who might have their own ideas about matters.
The King also had a fairly sizable income from Droits of the Crown and Droits of Admiralty , and maybe from the 4 1/2% customs on the Caribbean Islands (I'm not sure whether that was the case as early as this - certainly was by Geo III's time.
But all army commissions, Guards or Line, were in the gift of the King. One of Car II's earliest laws was to make any Parliamentary interference in the Army illegal. Parliament got to say how many troops, how much they got paid, and, broadly, where they were used. Everything else was the king's authority.
EDIT: The whole question of resumption of land grants, confiscations etc depends very much on how much like a re-conquest the event is. If Parliament offer James back the throne without any fighting, just a "Here y'go Your Majesty, sorry about the 26 year mix up" then the new King can't actually do that much . Like Car II . But if the new King is opposed , and has to fight his way to the throne (either personally or by proxy), then it becomes more of a conquest , and he has a lot more flexibility. F'instance, if James is opposed by military force, his first thing will be to send summonses to all the landowners , and chief towns , demanding they turn out to support him, "or be deemed my enemy, recreant , and your lands, charters etc forfeit". Most won't of course, some will actually oppose him, most will just want to wait and see. But, then, if he wins, he can go back to those who didn't support him when he called upon them and remind them about that forfeiture bit. So he actually does better ifg there is opposition. And, of course, opposition gives him a better chance to kill off his enemies.
OK so the Guard Regiments answered to the Crown. Good to know. And the Colonial Crown lands could be used to provide additional income, providing they were usable and not controlled by Indians. And the Droits were sort of like various feudal dues that the Crown used to collect or am I wrong? And the army was also the King's privilege, though with major advise from Parliament. Reading threw our discussion, it seems the Crown was in a better financial situation then I previously thought. Sure the Crown didn't have absolute power over finances, like Portugal or France, but the Crown wasn't totally dependent on Parliament like in later generations. What about Tonnage and Poundage? Was that still granted to the Monarch or no? Cause the latest I can find it being voted was James II.
So it would depend on if the Coup is successful and everyone accepts it or if a few Whig grandees escape London or weren't there in the first place and try to raise a rebellion. If its the later James would be in a stronger position. He can seize estates, ruin the Whig's as a political Party and eliminate potential enemies. I doubt the Whigs would be very popular considering they're fighting to bring the British Isles under the control of a foreign monarch. Not a good goal for a Nation that was notoriously xenophobic.