Twelve-string setup

I have a question for you about 12 strings guitar set up.
I do not have much experience in playing and setting up 12 strings guitars.

I am setting up a 12 strings guitar and I have found that is difficult to
press two strings, on the same row, that have different diameter with the
same pressure. So I find that if I press the fifth row of strings (0,039 - 0,018) I am able
to press the 0,039 string well but the 0,018 not so well and it rattles
because it is not pressed well. This happens also for the third, fourth an sixth rows (less in the sixth). This guitar has good action (1/16 & 3/32 at 12 fret).

1. Is it possible to reduce this difficulty installing higher frets (this
guitar has 0,04" tall frets).

2. Is it possible to reduce it setting each string row more apart?
(each row is more or less 1/16 apart at the nut and 3/32 apart at the
saddle). Which distance do you recommend?

3. Do you think that it is better to cut nut slots with different height in
the same row to gain more comfortable action at the first fret?

That's all.
I Hope you will find the time to answer me.

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The greatest clarity of sound on a 12-string is the not the result of fret height, or in a difference of slot-depth at the nut for each member of the string-pairs. In your case I see the following difficulties:

1- There is no getting around that a 12 string player has to develop more grip strength than a 6-string player. A beginning 12-string player will have clarity problems no matter what the string spacing or string set up is, until the player realizes that more muscle pressure is necessary to press both strings down firmly for a clear sound. It takes specific hand skills to play a 12-string expertly. So be assured that a weaker player will undoubtedly complain about clarity no matter how expertly made or set up the 12 string is. So as a builder or repair man, you must be ready for that dilemma and not blame yourself exclusively.

2- Your strings are indeed too closely spaced at the nut, if they are 1/16 inch (1.6 mm). That can also contribute to a lack of clarity if the strings clash together, the smaller string being overpowered by the larger. At the nut, the optimum spacing is an average of 3/32, with the trebles a tiny bit less and the basses a tiny bit more. At the bridge, the diameter of the bridge pins is a limiting factor, since it is not good practice to cut grooves into the saddle. However if your pins are very fat, you may make a clearance notch in the bridge pins to insure that the optimum spacing between the pairs is 1/8 inch.

3- Your action height is too low. The thinner string will be the first to be dampened when it strikes the frets. So what is the optimum height? Optimum is the highest action possible, given the limits of the players strength, that is, not so low that the strings jangle and rattle on the frets, yet not so high that the player can't press them all the way down. That's the dilemma: a beginning player will complain of difficult action even at a very low setting, which then makes the strings easily contact the frets; then complain about the lack of clarity. Expert 12-string players have a well-developed grip, but also have developed an instinctive ability to press the strings appropriately and efficiently no matter what the string height. But given the choice, they prefer a high action to a low because they are strong enough to overcome it, and it gives them a better tone and a wider dynamic range.

So the 12 string is not an appropriate instrument for a weak or beginning 6-string guitarist. So don't let them blame you for their own lack of development. You learn to play the 12 string guitar AFTER you have become a competent 6-string player. If a weak beginner insists on playing with a very low action, they must accept a sizzly, jangly, unclear sound until they become strong enough to play with a raised action.