Learn Farsi: ما جریمه را داخل گمرک پرداخت نکرده بودیم.

The verb is پرداخت کردن (to pay). For the negative past perfect ("had not paid"), we add the negative prefix نـ (na-) to the past participle of the light verb کردن, giving us نکرده (nakarde). Then we add the simple past form of بودن (to be) for "we", which is بودیم (budim). The noun part پرداخت stays unchanged at the front.

Why does the negative prefix نـ go on نکرده instead of پرداخت?

In Farsi compound verbs, grammar prefixes like the negative نـ (na-) or the continuous می (mi-) always attach to the "light verb" (here, کردن). They never attach to the non-verbal part (پرداخت).

Why is the object marker را used after جریمه?

را (ra) marks a specific direct object. Because the sentence means "had not paid the fine" (a specific fine they already know about) rather than just "a fine in general", we must place را directly after جریمه (jarime).

Do I need to pronounce an ezafe (the "-e" connector) after داخل?

Yes. When using داخل (dakhel), which means "inside", as a preposition before a noun, it requires the ezafe connector. You pronounce the phrase as .