Here is what I see as how the history of the infinity stones could work in the MCU.
The original background of the stones once being part of a galactic being would remain.
A group of beings was created, each with an infinity stone, they were tasked to stopping the stones falling into the wrong hands (the infinity watch), this included Warlock and Thanos.
In a battle with.....(this could be the villain for phase 4, or the Magus after an encounter with the mind and or soul stone splits Warlock in 2 or perhaps 2 Warlocks were created?) Thanos is nearly killed and the villain is only stopped by Warlock and the other infinity watch members. After Thanos nearly dies whilst wielding the mind stone he becomes convinced that Death saved him.
Thanos then studies the Infinity stones and come up with he's plan and tries to take the other stones from the other infinity watch members, he manages to kill the other infinity watch members but Warlock escapes with the other stones entrusting them to others (e.g. The reality stones to the dark elves).
Adam Warlock then goes into hiding as he knows who has the stones and does not want Thanos finding them, he does what he can to hide their power from Thanos (hence why he did not detect Hydra using them the tesseract in WW2), Loki then finds the tesseract and with the massive amounts of power used by the Tesseract in Avengers he can no longer mask the power of the infinity stones. (The infinity stones are linked, as one stone is used the power in the others builds not to significant levels but high enough so Thanos has a chance of finding them but even with he's technology he has limits and has to rely on scouting drones/parties using sophisticated scanning tech).
This could be dealt with by a Adam Warlock flash back.
And this is how I would have the 2 remaining infinity stones powers:
Time stone- Currently in possession of the Kree and is known as the future stone, they experimented with it trying to further their own evolution but instead froze their own evolution (this would explain why Ronan knew about the infinity stones after he gets the orb), it has the power to alter how time affects people so evolution, ageing etc. Without the power stone it would not allow time travel (or at least after the Kree got their fingers burnt they have not tried it/have knowledge to do it) until the villain goes after it.
Soul stone- Would not imprison people within it as the Mind stone already has a very similar power and as Marvel seem to want to stay down a more science based route (even with Dr Strange) then this would seem inappropriate, instead it would have the power to drain the life energy of any living thing within it, empowering the bearer, the soul stone would also be the key to making the infinity gauntlet (work the large central stone in the infinity gauntlet, so the time stone would be green and this would be orange), it contains the essence of the being that exploded to created the infinity stones, without it Thanos can only tap into the power of one stone at a time, this would lead to a plan where they try and distract Thanos whilst someone flies in a removes the large central stone.
The time stone would appear in GOTG 2, IF the Magus is the villain then he would want to use the time stone to reverse he's original defeat to infinity watch or he may just want to use it for other means.
Soul stone would be Dr Strange as the Eye of Agamotto.