The funny part of them all is the following - The Universe is made mostly of Hydrogen and Helium, Abundance in the Universe of the elements, but we still have planets and expect them to be not only in our star system.
The question is not how low is a percentage of elements we need, but how big is the thing where they are. The Sun, Sun Fact Sheet, is relatively big, 333'000 times mass of the Earth.
Major elements: H - 90.965%, He - 8.889%
Minor elements (ppm): O - 774, C - 330, Ne - 112, N - 102, Fe - 43, Mg - 35, Si - 32, S - 15
In fact, sun composition contains more than just 330ppm of carbon, but this concentration is on top of the sun, in upper layers (carbon is relatively heavy and it sinks to the core, but still some of it floats in upper layers).
This concentration is relatively big actually, it is 0.396% by mass, so to made one planet like Earth but made of pure carbon, you need to purify matter of about 250 mass of earth from upper layers of the sun. As a byproduct, you will get about 2 earth mass planets made of oxygen, about half mass pure neon planet, 0.6 mass from Fe etc.
If you combine those 2 oxygen planets with a proper amount of hydrogen - you will get about 2+ planets made of pure water.
And that all can be done just by barely scratching the sun, all you need it 0.1% of the sun.
Gas giants like in our system (we are lucky to have cold ones) are basically a small fragment of the star, and they have very similar composition.
Jupiter(Jupiter Fact Sheet), as an example, have the mass about 317.83 of the Earth, so basically it is a bit more than 250 masses you need to create a few planets made of pure elements.
In my the longest answer on WB.SE I began to describe the initial phase of the process, but answer limitation had effectively prevented to disclose all the details about the process. But it has some description how it can be done.
The main point is that to lift the matter from the star, you need a lot of energy, even by having all the energy of the star, but any matter which orbits the sun, may be effectively exchanged with the matter from the sun, because it already have all needed energy you may need to lift the matter from the star into the orbit around the star. Namely, it means all mass of the Jupiter(its hydrogen and helium) may be exchanged to heavier elements from the sun, and it will be enough to make about 300 planets like the earth.
But as you talking about tuning of a planet, you probably do not need the same scale of operation as in my longest answer on WB.SE
Water is not a problem at all because rocks are oxides of mostly silica, so any rocky planet can be made an ocean planet with the proper amount of hydrogen reacting with those rocks. (you better have space lift or space ring for that types of reaction, to not overheat the planet, and do the reaction in space). It may be a hardcore way of doing it, as there is a lot of water in asteroids, and it is guaranteed a lot of water in any system as Oxygen and Hydrogen are most abundant elements, and freezing point of water is pretty high. Water will form during the system formation and there will be a lot of water ice in a typical system(nearby supernovae blast may change the thing, not in favor of water ices but you always may go the hard way, making it from rocks and hydrogen from a star or gas giant).
Basically, all problems from your answer do not need - super intergalactic civilizations, elements transmutations, etc.
Would we have manufacturing in space and the wish to do so, we could do it ourselves, with technologies we already have. Maybe not from the sun but from gas giants for sure, with the sun we need a bit more advanced technology.
But really, you do not need terraforming's, build space habitats they are more efficient.