We spent about half a year learning about one themeopic, discussing it, and practicing a presentation.

'Theme' does make sense but 'topic' might work better here

It was a hard period for me because the members, except me, handledspoke English very well.

I'm assuming they were speaking English but correct me if I'm misinterpreting.

On the other hand, I'd only gone on a foreign triptrip abroad once.

What you said makes sense but 'trip abroad' is more commonly used

I met 5five of my high school friends yesterday in Tokyo.

Almost four years have passed since we last met.

Sentence is correct, but a more natural phrasing might be:
--> Casual: "It's been almost four years since we last met"
--> More grammatically correct: "It has been almost four years since we last met"

ItThis was a harddifficult period for me because the members, except me,everyone handled English very well, except for me.

One of my friends's father was French, and thwhile others had spent some years abroad.

I usually see phrasing like "one's father" in formal or academic writing.

On the other handConversely, I'd only gone on a foreign trip once.

Sentence was correct, but your writing is pretty good so this correction gives you a more advanced way to phrase this.

I met 5five of my high school friends yesterday in Tokyo.

It's customary to write out numbers 1-9 or 1-10 depending on the style guide you are using.

We have six members in our group, in fact, but one of us couldn't come this time.

In addition to the suggestions from other readers, you could use "actually." It is very close in meaning to "in fact" and works better in the sentence:
"Actually, We have six members in our group, but one of us couldn't come this time."
"We actually have six members in our group, but one of us couldn't come this time."

Another option is to use "Although" which changes the sentence structure because it introduces a subordinate clause (the part with "although" is subordinate, or less important than the main clause):
"Although we have six members in our group, one of us couldn't come this time."
"We have six members in our group, although one of us couldn't come this time."

We spent about half a year learning about one theme, discussing it, and practicing a presentation.

The feedback on the word "theme" is interesting. If that is what your program called it, then that, obviously, is the best term to use.
Both "topic" and "subject" can refer to very specific items. For example, both can be used in the expression "to change the topic/subject."
Themes can be more abstract, and sometimes they can be expressed in a phrase rather than a word.

It was a hard period for me because the members, except me,everyone else in the group handled English very well.¶
It was a hard period for me because I was the only group member who didn't handled English very well.

I think an argument can be made for keeping the verb "to handle." First, it implies other skills besides speaking. Second, it has a physical association that suggests the kind of awkwardness and difficulties you had due to your limited proficiency.

However, I guess that this experience changed my life, at least a little.

not needed

We spent about half a year learning about one themeopic, discussing it, and practicdoing a presentation.

"Theme" feels more... secondary? It's a little late and I'm a bit sleepy so it's hard for me to explain, but if a "topic" is like a wall, then a "theme" is like the paint on that wall.

AsFor the climax of this program, we visited the USA to meet a few specialists.

It was a hard period for me because the members,everyone there except me, handled spoke English very well.

On the other handMeanwhile, I'd only gone on a foreign trip once.

However, I guess that this experience has changed my life, at least a little.

I'm using the present perfect tense to emphasize that this is recent past. This isn't strictly necessary, but I think it sounds a little better.

It gahas given me the courage to communicate with people abroad in English.

(In fact,) We have six members in our group, in fact, but one of us couldn't come this time.

The sentence sounds more natural without "in fact", but if you'd like to keep it, it'd go at the beginning of the sentence.

We spent about half a year learning about one theme/subject, discussing it, and practicdoing a presentation.

You could use "theme" or "subject" here.

It was a hard period for me because all the members, except me, handled English very wellfor me, were very good at English.