Learn Farsi: کاش پازل‌های فیزیکی نظیر این جعبه را حل کرده بودیم. - I wish we had solved physical puzzles such as this box.

Nazir-e means "such as" or "like," and it connects to the noun phrase in ja'be (this box) using an ezafe. While it means the same thing as mesl-e or mānand-e, nazir-e is slightly more formal and is specifically used to introduce examples that belong to the broader category just mentioned (in this case, physical puzzles).

Could we use the phrase az qabil-e instead of nazir-e in this sentence?

Yes, they are practically interchangeable in this context. While nazir-e literally implies "the like of" or "similar to," and az qabil-e means "from the category of," both effectively mean "such as" and take an ezafe to introduce specific examples of a previously mentioned category.

Why does the direct object marker rā come all the way after in ja'be instead of right after the main noun phrase pāzel-hā-ye fiziki?

In Farsi, the postposition rā must attach to the very end of the entire noun phrase it marks. Because the phrase pāzel-hā-ye fiziki nazir-e in ja'be (physical puzzles such as this box) acts as a single, complex direct object, rā is placed at the very end of this entire block.

Why is the past perfect tense (hall karde budim) used here instead of a subjunctive form?

The word (I wish) expresses an unrealized desire. When you wish for something to be different in the past (a counterfactual past, like "I wish we had solved"), Farsi uses the past perfect tense. If you were wishing for something to happen right now or in the future, you would use the past subjunctive instead.