I think one of the biggest challenges with English is its flexibility. There are a couple of ways you could work that sentence. Here's one way:
- This sentence is a short version of a longer sentence which I've rewritten without changing the structure, and I'm confused with it.
You could also break it up:
- This sentence is a short version of a longer sentence. I've rewritten it without changing the structure. I'm confused with it.
To answer your question more directly, 1 and 2 are fine in the order they're in.
"Which" is an interesting word; usually it's used (as a determiner) when you're adding descriptive information about something: "This is my car, which has a 2.4l motor.", or "This cat, which is a tabby, eats a lot of cat food." If I were keeping your sentence a little more intact, I might write it like this:
- This sentence, which is a short version of a long version that I rewrote, keeping the sentence structure intact, is making me confused.
One other thing: you have two independent clauses in your sentence (and I apologize; this can be a little confusing):
- This is a sentence I wrote
- I am confused
Usually in English you would have two sentences, one for each clause, or you'd join them with a conjunction:
- This is a sentence I wrote, and I'm confused with it.
The weird thing here is that this clause:
. . . doesn't really count as a clause, because it's being used to describe the noun "sentence". So we treat that as a big adjective.
Anyway, I hope that's helpful, at least a little bit.