I don’t believe "il", "se" or "en" refer to anything specific in the expression "il s’en faut". It’s the way that expression is built.

For example imagine Jean wants to buy a 5 Euro bread but has only 3 Euros:

• Il s’en faut de deux Euros que Jean puisse acheter le pain.
• Il faut deux Euros de plus à Jean pour qu’il puisse acheter le pain.

The two sentences can be equivalent.

Unlike the answer that the first link in your question leads to, I don’t believe that s’en falloir de per se is an idiomatic expression, because it has not been declared as such in any dictionary I checked.

Let’s look at the following examples of the Dictionnaire de l’Académie française to understand better.

1. Il s’en faut de cent francs.
2. Peu s’en faut/ Peu s’en fallut qu’il ne fût expulsé.

(1.)
The meaning of example (1.) corresponds to the following explanation in the Dictionnaire de l’Académie française: "se dit pour indiquer une différence en moins".
So, instead of the (maybe more common) meaning of needing something ("Il faut de l’argent"), [s’en]falloir is used to express the lack of something. The only difference between the two meanings is the perspective, but as @Jonathan has said before, it might not be significant.

As il faut is a unipersonal verb, I would consider se to be a reflexive pronoun.

En refers to cent francs. According to Grevisse’s Le Bon Usage (Grevisse & Goosse 2008: 869), en can be seen as a complément de verbe which replaces the object indirect "de cent francs".
More precisely, the latter is the "sujet réel" of the unipersonal verb falloir (cf. Grevisse & Goosse 2008: ibid.).

(2.)
The second example is, in fact, a fixed expression because of its ancient, non-modifiable structure, which becomes evident when looking at the omission of the impersonal pronoun ("il") and its substitution for the sujet réel which is an indefinite pronoun ("peu") (Grevisse & Goosse 2008: 395).

Edit:

In response to the comment of @jlliagre, I tried to render my thoughts regarding the issue of whether or not il faut (and consequently s’en falloir) is an idiomatic expression more precisely.
I think what is described in the comment is "just" a syntactic expletive which exists in so-called pro-drop languages. It occurs not only in French but also in other languages, for example Spanish (Llueve.), English (It rains.) and German (Es regnet. Note: I recommend the examples in the german version of this Wikipedia Website but it exists as well in French and English).
In addition, as I understand Gregor Perko, the degree of figement is (arguably) not high enough in the case of "il faut".
In Dictionnaire des Gallicismes, there are only chosen expressions with falloir, for example "comme il faut". The same applies to pleuvoir and neiger. Recent dictionaries and grammars (Larousse, Le Robert, Le Bon Usage and Littré) proceed in the same manner.

Grevisse, Maurice & Goosse, André ([14]2008): Le Bon Usage. Grammaire Française. Bruxelles: Éditions de Boeck Université.