Det står rena glas i skåpet, men min mugg står fortfarande på diskbänken.

Because Swedish often uses a position verb when talking about where things are.

In English, we often just say there are clean glasses in the cupboard.
In Swedish, it is very common to say:

• det står for things that are standing upright
• det ligger for things lying down
• det sitter for things attached or seated

So Det står rena glas i skåpet is a very natural way to say that clean glasses are there in the cupboard.

You can sometimes use det finns for simple existence, but det står sounds more specific and idiomatic here.

Because both the glasses and the mug are being imagined as upright objects resting on a surface.

In Swedish:

• cups, glasses, bottles, and similar containers usually står
• flat things like papers or plates may ligga
• things attached to something may sitta

So:

• Glasen står i skåpet
• Muggen står på diskbänken

Even though the glasses are in the cupboard, they are still thought of as standing on the shelf inside it.

Because the adjective has to agree with the noun.

The adjective ren changes form like this:

• en ren mugg
• ett rent glas
• rena glas

Here, glas is plural, so the adjective becomes rena.

A useful detail: rena is also the form used with definite nouns, but here it is plural agreement.

Here it is plural.

The word glas is one of those Swedish nouns that often has the same form in singular and plural:

• ett glas = a glass
• två glas = two glasses

So how do you know it is plural here?

Because of the context and especially the adjective:

• ett rent glas = one clean glass
• rena glas = clean glasses

The plural adjective form tells you that glas is plural in this sentence.

Because mugg is an en-word.

Swedish possessives change depending on gender and number:

• min
  • en-word singular
• mitt
  • ett-word singular
• mina
  • plural

So:

• min mugg
• mitt glas
• mina muggar

Since mugg is en mugg, the correct possessive is min.

Because after a possessive like min, mitt, mina, the noun is usually in the indefinite form.

So Swedish says:

• min mugg = my mug
• mitt glas = my glass
• mina glas = my glasses

Not:

• min muggen
• mitt glaset

This is a very important pattern in Swedish: possessives normally replace the definite ending.

Because Swedish uses different prepositions depending on the type of location.

• i = in / inside
• på = on / on top of

So:

• i skåpet = inside the cupboard
• på diskbänken = on the counter / on the sink bench

This matches the physical idea:

• the glasses are inside the cupboard
• the mug is on the countertop

They are the definite forms of the nouns.

In Swedish, the definite article is usually added as a suffix:

• ett skåp = a cupboard

• skåpet = the cupboard

• en diskbänk = a kitchen counter / sink bench
• diskbänken = the kitchen counter / sink bench

So:

• i skåpet = in the cupboard
• på diskbänken = on the counter

This is one of the big differences from English, where the is a separate word.

Fortfarande means still.

So:

• min mugg står fortfarande på diskbänken
  = my mug is still on the counter

Its position is normal for a Swedish main clause: it comes after the finite verb står.

Compare:

• Muggen står fortfarande där.
• Jag är fortfarande trött.

So the placement in the sentence is very natural.

No. Men is a coordinating conjunction, so the clause after it keeps normal main clause word order.

That means:

• men min mugg står fortfarande på diskbänken

with the subject min mugg before the verb står.

So this is just ordinary Swedish word order:

• subject + verb + adverb + place

If something else had been put first for emphasis, then the word order could change, but here it stays straightforward.

Yes, ren can also mean pure in some contexts. But in this sentence, rena glas clearly means clean glasses.

For example:

• rent vatten = pure water
• rena kläder = clean clothes
• rena glas = clean glasses

So the exact meaning depends on context, and here the kitchen setting makes clean the natural reading.