Ja radije mijesim tijesto rukama, jer mi to pomaže da se opustim.

Yes. In Croatian, the verb form mijesim already tells you the subject is I, so Ja is not required.

• Mijesim = I knead / I am kneading
• So Ja mijesim and mijesim can both mean I knead

Including Ja usually adds:

• emphasis
• contrast
• a slightly more personal tone

So here, Ja radije mijesim... can feel like:

• I prefer kneading...
• or even As for me, I prefer kneading...

Without Ja, the sentence would still be perfectly natural:

• Radije mijesim tijesto rukama...

Radije means rather or preferably, and in this sentence it expresses preference.

So:

• radije mijesim = I would rather knead / I prefer kneading

It is related to the adjective rado in the sense of doing something willingly, but radije is the comparative form:

• rado = gladly, willingly
• radije = rather, preferably

Examples:

• Radije pijem čaj nego kavu. = I’d rather drink tea than coffee.
• Radije ostajem kod kuće. = I prefer staying at home.

Because radije modifies the verb, so it usually goes before it.

• Ja radije mijesim tijesto rukama.

This is the most natural neutral order. Croatian word order is flexible, but this placement is very common when saying what you prefer doing.

You may also hear other orders for emphasis, but they can sound more marked:

• Ja mijesim tijesto radije rukama — less natural here
• Radije ja mijesim tijesto rukama — possible if contrasting with someone else

So for learners, radije + verb is a good default pattern.

Mijesim is the 1st person singular present tense of the verb mijesiti (to knead).

So:

• ja mijesim = I knead / I am kneading
• ti mijesiš = you knead
• on/ona/ono mijesi = he/she/it kneads

In Croatian, the present tense can often cover both:

• a general/habitual meaning: I knead
• an ongoing meaning: I am kneading

Here it sounds more like a general preference or habit.

Croatian often expresses this kind of preference with radije + present tense verb, where English might use prefer to + infinitive or prefer + -ing.

So instead of a very literal structure like:

• I prefer to knead

Croatian naturally says:

• Radije mijesim
  literally something like I rather knead

This is a normal and common Croatian pattern.

Tijesto is in the accusative singular, because it is the direct object of mijesim.

You are kneading what?

• tijesto

The dictionary form is the nominative singular, and for many neuter nouns, nominative and accusative singular are identical.

So:

• nominative: tijesto
• accusative: tijesto

That is why it does not change in form here.

Rukama is the instrumental plural of ruka (hand).

It is used because Croatian often uses the instrumental case to express the means or instrument by which something is done:

• rukama = with (the) hands / by hand

So:

• mijesim tijesto rukama = I knead the dough with my hands

This is a very typical use of the instrumental.

A quick mini-paradigm:

• singular: ruka
• plural nominative: ruke
• plural instrumental: rukama

Because when talking about doing something with your hands in a general physical sense, Croatian normally uses the plural, just as English usually says with my hands rather than with my hand.

So:

• rukama = with my hands

If singular were used, it would suggest one hand specifically, which is not the intended meaning here.

Also notice that Croatian often does not need a possessive pronoun where English uses one. So rukama naturally implies with my hands from the context, without needing svojim rukama.

Mi is the dative singular form of the pronoun ja, and here it means to me.

So:

• to mi pomaže = that helps me
• literally: that helps to me

The verb pomagati / pomoći takes a dative object for the person being helped.

Examples:

• Pomaže mi. = It helps me.
• Pomaže mu. = It helps him.
• Pomaže nam. = It helps us.

So in this sentence:

• jer mi to pomaže = because that helps me

To means that or it, and it refers back to the whole previous idea:

• kneading the dough by hand

So:

• Ja radije mijesim tijesto rukama, jer mi to pomaže... = I prefer kneading dough with my hands, because that helps me...

It is a very natural way in Croatian to refer back to an action or situation with to.

After many verbs and expressions, Croatian often uses da + present tense where English might use an infinitive.

So English:

• it helps me relax

Croatian:

• pomaže mi da se opustim
• literally: helps me that I relax

This is completely normal Croatian structure.

You will often see:

• Želim da dođeš. = I want you to come.
• Pomaže mi da bolje spavam. = It helps me sleep better.

So da + present is something learners should get used to.

Because the verb here is opustiti se, which means to relax.

The se is part of the verb. Many Croatian verbs are reflexive or use se in ways that English does not.

So:

• opustiti by itself can mean to loosen / release
• opustiti se = to relax

That is why you must say:

• Želim se opustiti.
• Pomaže mi da se opustim.

Without se, the meaning would change.

This is about aspect.

• opustiti se = perfective = to relax, to become relaxed, to achieve relaxation
• opuštati se = imperfective = to be relaxing, to relax in an ongoing/repeated sense

In the sentence:

• pomaže da se opustim

the perfective opustim sounds natural because the idea is that the action helps you reach a relaxed state.

If you used da se opuštam, it would focus more on the ongoing process of relaxing rather than the result.

Both aspects can make sense in some contexts, but da se opustim is very natural here.

Yes. Both can mean because.

So you could say:

• Ja radije mijesim tijesto rukama, jer mi to pomaže da se opustim.
• Ja radije mijesim tijesto rukama, zato što mi to pomaže da se opustim.

In many everyday contexts, jer is shorter and very common.
Zato što can sound a little fuller or more explicit, but both are standard.

Croatian word order is fairly flexible, but not all orders sound equally natural.

The original sentence is very natural:

• Ja radije mijesim tijesto rukama, jer mi to pomaže da se opustim.

You could also say:

• Radije mijesim tijesto rukama, jer mi to pomaže da se opustim.
• Tijesto radije mijesim rukama, jer mi to pomaže da se opustim.

But changing the order usually changes the emphasis:

• Ja at the start emphasizes I
• radije before the verb emphasizes the preference
• rukama near the end gives the method in a natural place
• mi is an unstressed clitic, so it tends to appear early in its clause: jer mi to pomaže

So yes, word order is flexible, but the original order is a very good model to follow.