The majority of the paper seems unused in the proof of the Collatz Conjecture. Your proof appears to be:
Step 1 (Theorem 3.6): For any $x \in \mathbb{Z}^+$, if we apply the Collatz transformation repeatedly $x,T(x),T^2(x),\ldots$, we eventually reach an element congruent to $1 \pmod 8$.
Step 2 (Proposition 3.2): If $x \equiv 1 \pmod 8$, then $x \mapsto 3x+1 \mapsto (3x+1)/2 \mapsto (3x+1)/4$ where $(3x+1)/4 < x$ provided $x>1$. This is also true.
Step 3: Repeatedly apply Step 2 until you hit $1$.
However, even if $x \equiv 1 \pmod 8$, it doesn't imply $(3x+1)/4 \equiv 1 \pmod 8$. E.g. $(3 \times 9+1)/4=7 \equiv -1 \pmod 8$. So, we can't repeatedly apply Step 2.
[Correction: I originally wrote "This can be verified via elementary number theory" in regards to Step 1, but I no longer think this is true, either. For example, starting from $433$, we get the sequence (mod 8):
1, 4, 2, 5, 0, 0, 4, 2, 5, 0, 4, 6, 7, 6, 3, 2, 5, 0, 0, 0, 4, 2, 5, 0, 0, 4, 2, 1
in which we don't hit $1 \pmod 8$ until right at the end (when we reach 1 itself). But, for the sake of argument, let's assume Step 1 has been proved.]