Ok, so the overall structure is like this:

> （[a]…たとえで言ったら、）　僕にとって「もてたい」ってやつは　人参でも[b]…程の人参だった。

*(Using the metaphor [a],) for me, "I want to be popular" was a carrot, (not just an ordinary carrot, but) a carrot like [b].* 


The first part of the sentence goes:

> 馬の前に人参をぶら下げて走らせるたとえで言ったら

Lit. *If I say regarding the metaphor where you dangle a carrot in front of a horse to get it to run,*. This may sound verbose, probably because the "carrot and stick" symbolisation is less frequent in Japanese. 

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> 僕にとって「もてたい」ってやつは　…人参だった

*For me, "I want to be popular (among girls: assuming this guy is heterosexual man)" was the carrot.*

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> 人参でも無農薬有機栽培の人参、グルメレポーターが食べたら、「これはフルーツですか？」とよくわからないけど何かすごそうみたいなコメントを言ってしまう程の人参

This part is tricky (and creative), but it just emphasises  what a great carrot (i.e. motivation) it [the desire to be popular] is. Let's read it bit by bit.

> 人参でも (1)無農薬有機栽培の人参、(2) [グルメレポーターが食べたら…程の]人参

Among carrots, it's (1) an organic carrot, (2) a carrot so amazing that...

無農薬有機栽培 vegetables are, in general, considered of a higher quality, more expensive, tastier, classier, etc. I'm guessing this is the same anywhere.


> グルメレポーターが食べたら、

*when a gourmet reviewer eats it* --- (Imagine, a TV show, where a cast eats an carrot, and says...)


>「これはフルーツですか？」と…コメントを言ってしまう

*"Is this a fruit?"*  ("Hey, this carrot is so sweet and tasty as it is --- it's like eating a fruit of some sort!")


> 「よくわからないけど何かすごそう」みたいな

which (the comment above) is actually like "I don't really understand the detail, but it seems great".


This part about the gourmet reporter might need an explanation. At least in Japan, we often see TV shows where the clues visit farmers, eat their product, and get amazed at how tasty they are, especially sweet, surprisingly so when compared to vegetables we buy at supermarkets. <small>{I'm somehow feeling that the same thing goes in other countries as well...}</small> The 「よくわからないけど何かすごそう」 part is a slightly cynical reference to these casts, who don't necessarily appreciate the real difference. 

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Anyway, to sum up --- 

> *Consider the metaphor, where you dangle a carrot in front of a horse to get it to run: For me, "I want to be popular" was the carrot --- an organic one, that kind of carrot which they say "Is this a fruit?" ---which is like "I don't understand well but it seems great"--- in the gourmet programmes on TV.*