Mi dankas vin pro via honesteco, ĉar nun mi scias kion fari.

Because danki takes a direct object in Esperanto. The person you thank is marked with -n:

• Mi dankas vin = I thank you

So vin is the object form. In standard Esperanto, you normally do not say Mi dankas al vi for this meaning.

Pro means for, because of, or on account of. It introduces the reason for the thanking:

• pro via honesteco = for your honesty / because of your honesty

So the sentence first gives a noun phrase as the reason, and then adds a full clause with ĉar.

Because via honesteco comes after the preposition pro. In Esperanto, prepositions normally take the basic form of the noun phrase, not the accusative -n.

So:

• pro via honesteco = correct
• pro vian honestecon = not correct here

Also, the possessive via matches the noun it belongs to, so if honesteco has no -n, then via also has no -n.

The suffix -ec- makes an abstract quality or state.

• honesta = honest
• honesteco = honesty

So honesteco is not a person or an act; it is the quality of being honest.

They are similar, but they work differently.

• pro is followed by a noun phrase:
  pro via honesteco
• ĉar is followed by a full clause with a verb:
  ĉar nun mi scias kion fari

So the sentence gives two linked ways of expressing the reason:

• for your honesty
• because now I know what to do

This is completely natural.

Because ĉar introduces a subordinate clause, and it is very common to separate that clause with a comma.

So:

• Mi dankas vin pro via honesteco, ĉar nun mi scias kion fari.

This helps show the structure clearly. Esperanto punctuation is fairly flexible in some cases, but this comma is standard and natural.

Because kion is the object of fari.

Think of it as:

• fari ion = to do something
• kion fari = what to do

The -n on kion shows that what is the thing to be done. Without -n, kio would not fit the grammar here.

Because Esperanto infinitives do not use a separate word like English to. The infinitive is shown by the verb ending -i.

• fari = to do
• scii = to know
• danki = to thank

So kion fari literally contains the infinitive in fari.

Yes. Both are possible, but they are slightly different in style.

• kion fari = what to do
• kion mi faru = what I should do / what I am to do

The version with just the infinitive is shorter and very natural after verbs like scii. The version with mi faru is more explicit.

Because kion fari is an indirect question, not a ke-clause.

Use ke for that-clauses:

• Mi scias, ke li venos. = I know that he will come.

Use a question word like kio/kion/kie/kial for indirect questions:

• Mi scias kion fari. = I know what to do.

So ke would not be used together with kion here.

Because Esperanto often uses the present tense for what English expresses as I thank you.

• Mi dankas vin is the normal way to say Thank you in a full sentence.

The present tense here does not have to mean an ongoing action in a narrow sense; it is just the standard way to express the act of thanking.

Not completely. Esperanto word order is fairly flexible, as long as the grammar stays clear. For example, nun could move:

• ĉar nun mi scias kion fari
• ĉar mi nun scias kion fari

Both are understandable. The version in the sentence is natural and emphasizes now nicely.