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sie isst = she eats / she is eating
sie (lower case) essen = they eat / they are eating
Sie (upper case) essen = you (formal) eat / you (formal) are eating
At the start of a sentence and in spoken language, the last two are identical. You need to look at the context to decide which one it is.
Sie can not be conjugated - it's a pronoun. Only verbs are conjugated.
Does "Sie" take third party verb conjugations? No. "Sie" is actually second party but it's verbs' conjugated form is the same as the infinitive form; however, "sie" is third party and it's conjugation is dependent upon it's meaning - sie isst for she eats and sie essen for they eat.
They don't sound the same. "ihr" sounds similar to English "ear" and "er" sounds similar to English "air" (imagine a British/RP accent).
Not to sound curt, but this is been widely discussed. German words have gender - masculine, neuter, and feminine. One learns a word with gender. For example, the word for apple is "der Apfel". One should never learn the word without the gender. The words der, die, das, den, dem, des show gender and case (nominative, accusative, dative, and genitive). Try readying through some of the discussions and perhaps it will become more clear. Good luck.
First of all, ihr is the subject of the sentence; therefore, it is in the nominative case. In nominative case, ihr can only mean you (informal plural). It could never mean "she", which is actually "sie". Also, the verb conjugation can only be used with second-person plural, which is "ihr".