Learn Hardcore Japanese: kinou ha densya ga tomaranakute yokatta to omoimasita. - I was glad that the train didn’t stop yesterday.

Using 昨日は can imply a slight contrast, like “Yesterday (at least) the train didn’t stop (maybe other days it did)” or just “speaking about yesterday in particular”.
Time expressions like 今日, 昨日, 明日 often take は when they are used as the topic of what you’re about to say.

Why is it 電車が and not 電車は?

が marks 電車 as the grammatical subject: the train is the thing that didn’t stop.

電車が止まらなくてよかった。
→ It was good that the train didn’t stop.

If you say:

電車は止まらなくてよかった。

then 電車は becomes a topic and often carries a contrast nuance, like:

As for the train, it didn’t stop (but maybe something else did).

In your sentence, the natural focus is simply “the train didn’t stop”, not “as for the train (in contrast to other things)…”, so 電車が is the most neutral and common choice.

What exactly is 止まらなくて? How is that form made?

止まらなくて is the て-form of the negative:

Dictionary form: 止まる (to stop)
Plain negative: 止まらない (does not stop / did not stop, depending on context)
て-form of ない:
ない is an い-adjective, so
ない → なくて (like たかい → たかくて)
Combine: 止まらない → 止まらなくて

So structurally:

止まる → 止まらない → 止まらなくて

In this sentence, V-なくて + よかった forms a pattern meaning “I’m glad that (something) didn’t V.”
So 止まらなくてよかった = I’m glad it didn’t stop.

Why 止まらなくて and not 止まらないで? Are they different?

Both V-なくて and V-ないで are negative connectors, but they have slightly different typical uses.

V-ないで often means “without doing V”:
- 朝ごはんを食べないで学校に行きました。
  → I went to school without eating breakfast.
V-なくて often emphasizes a reason/cause or condition:
- 雨が降らなくてよかった。
  → It was good because it didn’t rain.

In the pattern V-なくてよかった, なくて is the standard, set expression for:

I’m glad that [negative event] didn’t happen.

You can sometimes hear 止まらないでよかった, and people will understand it, but:

止まらなくてよかった sounds more natural for an event outside your control (the train’s behavior).
～ないで is more strongly associated with “doing something without doing V” (your own intentional action).

So here, 止まらなくてよかった is the usual, natural phrasing.

What does ～てよかった really mean? Why is it よかった in the past?

V-てよかった means roughly “I’m glad (that) I / it V-ed” or “It was good that V happened.”

早く家に帰ってよかった。
→ I’m glad I went home early. / It was good that I went home early.

In Japanese, よかった is the past tense of よい / いい (good).
The idea is:

Something happened (or didn’t happen) in the past.
Looking back, the result of that is good.
So you say “it was good (that X happened)” → ～てよかった.

Even if in English you’d say “I’m glad…”, Japanese expresses it as a past evaluation: “It was good that…”.

So 止まらなくてよかった literally is:

It was good that (the train) didn’t stop.

which in natural English is “I’m glad the train didn’t stop.”

Could I say 昨日は電車が止まらなくてうれしかった instead of よかった? What’s the difference?

Yes, you can say:

昨日は電車が止まらなくてうれしかった。

This means “I was happy that the train didn’t stop yesterday.”

Nuance:

～てよかった
→ Focuses on the situation being good / fortunate. It’s a bit more objective or situational.
～てうれしかった
→ Focuses on your personal emotion, your happiness.

In your original sentence, 止まらなくてよかった emphasizes that the fact the train didn’t stop was a good thing (convenient, fortunate, etc.).
止まらなくてうれしかった puts more focus on “I felt happy.”

What is the function of と before 思いました?

The と is the quoting particle. It marks what you thought.

The structure is:

[Clause] + と + 思いました

Here, the clause being “quoted” inside your mind is:

昨日は電車が止まらなくてよかった

So literally:

昨日は電車が止まらなくてよかった と 思いました。
→ (I) thought: “It was good that the train didn’t stop yesterday.”

と is used like this with verbs of saying, thinking, feeling, etc.:

言う (to say): そうだと言いました。
思う (to think): 彼は優しいと思います。
感じる (to feel): 変だと感じました。

Without と, 思いました would not clearly know what its content is, so you need と here.

Why is it 思いました (past) and not 思います (present)?

思いました marks the act of thinking as something that happened at that time in the past (yesterday or when you realized it).

昨日は電車が止まらなくてよかったと思いました。
→ Yesterday, I thought “It was good that the train didn’t stop.”

If you say:

電車が止まらなくてよかったと思います。

that’s more like:

I think (in general / now) that it was good the train didn’t stop.

Mixing 昨日は with 思います is possible but usually feels odd, because 昨日 is a specific past time, while 思います describes your current or general opinion.

So:

Talking about what you thought at that time → 思いました
Stating your current opinion now → と思います (usually without a specific past time adverb like 昨日)

Why is there no word for “I” in the sentence? Where is the subject of 思いました?

Japanese often omits pronouns like “I”, “you”, “he”, when they are clear from context.

In this sentence:

思いました is in polite form.
In ordinary conversation, the default assumption is that the speaker is talking about their own thoughts unless something else is said.

So (私は) 昨日は電車が止まらなくてよかったと思いました。 is understood as:

私は = “I” (implied, omitted)
→ I thought it was good that the train didn’t stop yesterday.

You only add 私 (or another explicit subject) when you need to clarify or contrast, e.g.:

私はそう思いましたが、彼はそう思いませんでした。
→ I thought so, but he didn’t.

Is there any difference between writing 止まる and 停まる for trains?

Both 止まる and 停まる are read とまる, but the nuance is slightly different:

止まる
- More general “to stop” (stop moving, stop an action).
- Very common, default choice.
停まる
- Often used for vehicles, trains, etc., stopping at a place/station.
- Emphasizes a stop at a designated point.

In practice:

For trains, you will see both 電車が止まる and 電車が停まる.
止まる is more common in everyday writing and is perfectly natural here.
停まる can feel a bit more technical/precise or formal, but is not required.

So your sentence is completely fine with 止まる.

Can I change the word order, like 電車が昨日は止まらなくてよかったと思いました?

You can move elements around in Japanese, but not all orders sound equally natural.

昨日は電車が止まらなくてよかったと思いました。
→ Very natural.
電車が昨日は止まらなくてよかったと思いました。
→ Grammatically possible, but sounds somewhat marked/awkward.
It may sound like you are putting special contrastive focus on 昨日は after introducing the train, which is unusual.

Time expressions like 昨日, when used as a topic with は, are very commonly placed near the beginning:

昨日は電車が止まらなくてよかったと思いました。
昨日、電車が止まらなくてよかったと思いました。

So it’s best to keep 昨日は at or near the start.

Would 昨日は電車が止まらなくてよかったです be okay? How is it different from …よかったと思いました?

Yes, this is also correct:

昨日は電車が止まらなくてよかったです。

Differences:

With 思いました
- 昨日は電車が止まらなくてよかったと思いました。
  → I thought it was good that the train didn’t stop yesterday.
- You are explicitly talking about your thought at that time.
Without 思いました, with です
- 昨日は電車が止まらなくてよかったです。
  → I’m glad the train didn’t stop yesterday / It was good that the train didn’t stop yesterday.
- You directly state your evaluation/feeling to the listener.
- です makes it polite.

In everyday conversation, 昨日は電車が止まらなくてよかったです is a very natural way to simply say “I’m glad the train didn’t stop yesterday.”
The version with と思いました sounds a bit more like you’re reporting what went through your mind at that time.