When you use Wrath of the Storm with Thunderbolt Strike, the creature that attacked you is pushed back immediately. From the section on reactions:
If the reaction interrupts
another creature’s turn, that creature can continue its
turn right after the reaction.
The creature doesn't get to finish its turn, then get hit by your reaction - your reaction happens straight away, interrupting their turn. So if you use Wrath of the Storm + Thunderbolt Strike on the 1st attack of a Multiattack, the creature will be pushed back 10 feet.
Then, if it has movement remaining, it can move up to you and finish its Multiattack sequence. If it does not have enough movement to get back within reach of you, it will have to either end its turn without completing its Multiattack, or take the other attack(s) on a creature that is within its reach.
First of all, there is nothing in the spell description that suggests that "control over the existing storm instead of creating a new one" does anything other than subvert rather than create the same "storm cloud" described in the first paragraph. If there is already a cloud 100 feet above your head you get that one (and the extra damage); if not, you create one. So the answer to your question is the same in both cases.
The spell's description says:
When you cast the spell, choose a point you can see
within range [120 feet]. A bolt of lightning flashes down from the
cloud to that point. ... On each of your
turns until the spell ends, you can use your action to call
down lightning in this way again, targeting the same
point or a different one.
There are two things to consider:
Range
The target of a spell must be within the spell’s range.
Once a spell is cast, its effects aren’t limited by its
range, unless the spell’s description says otherwise.
"in this way again" means that range is still a factor. And this tweet (apart from the fact that the range is misquoted) indicates that the range is measured from you - not your storm cloud:
@mikemearls As a follow-up, as long as you can see a target within that 60 ft. radius, you can move as far away from the storm as you want?
@TheShieldComics Yes
Target
To target something, you must have a clear path to it,
so it can’t be behind total cover.
I think that in the case of this spell it is the cloud, rather than you, that must have the clear path.
Is there a restriction on the location of where the spell caster can call lightning down from when the lightning is called down from a natural storm in stormy weather?
Yes, the target must be within 120 feet of you and have a clear path to the cloud
So yes you can do exactly what you want - move up to 3000 feet and keep calling lighting from your pet cloud that is 3000 feet away. Given that a lighting leader travels at 61 km/s and the return stroke at 27,800 km/s; the lighting will take about 15 milliseconds to make the journey - well within the 6 second round. You can do this irrespective of if there was a pre-existing storm or not.
Best Answer
I did some digging into this particular question and I came up with these relative links.
First and foremost: This one about what happens if you lose line of sight
Followed by this very informative entry here on our very own Stack Exchange: About how you can keep concentration on a spell regardless of line of sight, range to the target(s) or AoE, or even plane of existence.
To answer your question directly, though; yes, there is nothing stopping you (neither in the spell description or rules on concentration and spell casting) from casting Call Lightning and then maintaining it's effects for a full 10 minutes even as your ship drifts away from the storm cloud.
For a more in depth look at the spell, here are a few key points.
I may be wrong (and anyone is free to leave potential corrections), but from all the above resources I've gathered, we seem to be able to conclude the following: You may cast Call Lightning and as long as you do not break concentration; you may continue to call down the full wrath of it's power for 10 minutes, even if you were to be taken to the Ethereal Plane (as per the spell Blink). You only require line of sight to the point you can see that you wish to strike each turn, and the spell only requires that point in question be within 120ft of you, not the 60ft cloud it summons forth.