Ik wil het document vandaag downloaden, maar de website is zo langzaam dat ik er lang op moet wachten.

Because willen is a modal verb, and in Dutch modal verbs usually take a bare infinitive at the end of the clause.

So:

• Ik wil downloaden
• Ik kan komen
• Wij moeten wachten

In a main clause, the conjugated verb goes in second position, so wil comes early, and downloaden goes to the end.

After modal verbs such as willen, kunnen, moeten, mogen, and zullen, Dutch uses the infinitive without te.

So you say:

• Ik wil downloaden
• Ik moet wachten
• Zij kan komen

not:

• Ik wil te downloaden
• Ik moet te wachten

The word te is used in other infinitive constructions, but not after modal verbs.

Zo ... dat means so ... that.

Here:

• zo langzaam = so slow
• dat ik er lang op moet wachten = that I have to wait a long time for it

So the pattern is:

• zo + adjective/adverb + dat + clause

Examples:

• Het is zo koud dat ik binnen blijf.
  = It is so cold that I stay inside.
• Hij praat zo snel dat ik hem niet kan volgen.
  = He speaks so fast that I cannot follow him.

Because langzaam is used here as a predicate adjective, after is:

• de website is langzaam

Predicate adjectives do not take -e in Dutch.

Compare:

• de langzame website = the slow website
  Here the adjective comes before the noun, so it usually takes -e.
• de website is langzaam = the website is slow
  Here it comes after is, so there is no -e.

Because dat introduces a subordinate clause, and in Dutch subordinate clauses the verbs usually go to the end.

So:

• Main clause: Ik moet wachten.
• Subordinate clause: ... dat ik moet wachten.

In your sentence:

• dat ik er lang op moet wachten

Both verbs are at the end of that clause, which is normal Dutch word order.

Here er is part of a pronominal adverb: er ... op.

The verb is wachten op = to wait for.
If the thing you are waiting for is not repeated as a full noun, Dutch often uses:

• erop = for it / on it / about it, depending on the verb and preposition

So:

• Ik wacht op het document.
• Ik wacht erop. = I’m waiting for it.

In your sentence, er refers back to something understood from the context, such as the download or the document.

In simple sentences, they often stay together:

• Ik wacht erop.

But they can be split when other words come between them:

• Ik wacht er al uren op.
• Ik moet er lang op wachten.

That is exactly what happens here. The adverb lang is placed between er and op, so you get:

• er lang op

This is very common and natural in Dutch.

Because lang is an adverb here, modifying the verb phrase op wachten.

• lang wachten = to wait a long time

Adverbs do not take -e.

Compare:

• een lange wachttijd = a long waiting time
  Here lange is an adjective before a noun.
• ik moet lang wachten = I have to wait a long time
  Here lang is an adverb.

So in your sentence, lang is correct.

Because Dutch nouns have different grammatical genders/classes, and singular nouns normally take either de or het.

• het document
• de website

Unfortunately, this often just has to be learned with the noun. There are some patterns, but many nouns must simply be memorized together with their article.

A good habit is to learn nouns as a full unit:

• het document
• de website
• de tafel
• het huis

Yes. Dutch allows some flexibility with adverbs like vandaag, although the emphasis can change slightly.

Your version:

• Ik wil het document vandaag downloaden.

Also possible:

• Ik wil vandaag het document downloaden.
• Vandaag wil ik het document downloaden.

All of these are grammatical. The choice depends on what you want to emphasize or what sounds most natural in context.

Because maar means but, and it introduces a contrast.

The sentence contrasts:

• I want to download the document today with
• the website is so slow that I have to wait a long time

So maar is the natural choice.

Want means because, and it gives a reason rather than a contrast. For example:

• Ik blijf thuis, want ik ben ziek.
  = I’m staying home because I’m sick.

In your sentence, the relationship is not just reason; it is mainly contrast, so maar fits better.