I don't think that

torsion in the homology has been ruled out

Certainly, torsion in Cech *cohomology* has been ruled out for a compact subset. The "usual" universal coefficient formula, relating Cech cohomology to $\operatorname{Hom}$ and $\operatorname{Ext}$ of Steenrod homology, is not valid for arbitrary compact subsets of $\Bbb R^3$ (although it is valid for ANRs, possibly non-compact). The "reversed" universal coefficient formula, relating Steenrod homology to $\operatorname{Hom}$ and $\operatorname{Ext}$ of Cech cohomology is valid for compact metric spaces, but it does not help, because $\operatorname{Ext}(\Bbb Z[\frac1p],\Bbb Z)\simeq\Bbb Z_p/\Bbb Z\supset\Bbb Z_{(p)}/\Bbb Z$, which contains $q$-torsion for all primes $q\ne p$. (Here $\Bbb Z_{(p)}$ denotes the localization at the prime $p$, and $\Bbb Z_p$ denotes the $p$-adic integers.
The two UCFs can be found in Bredon's *Sheaf Theory*, 2nd edition, equation (9) on p.292
in Section V.3 and Theorem V.12.8.)

The remark on $\operatorname{Ext}$ can be made into an actual example. The $p$-adic solenoid $\Sigma$ is a subset of $\Bbb R^3$. The zeroth Steenrod homology $H_0(\Sigma)$ is isomorphic by the Alexander duality to $H^2(\Bbb R^3\setminus\Sigma)$. This is a cohomology group of an open $3$-manifold contained in $\Bbb R^3$, yet it is isomorphic to $\Bbb Z\oplus(\Bbb Z_p/\Bbb Z)$ (using the UCF, or the Milnor short exact sequence with $\lim^1$), which contains torsion. Of course, every cocycle representing torsion is "vanishing", i.e. its restriction to each compact submanifold is null-cohomologous within that submanifold.

By similar arguments, $H_i(X)$ (Steenrod homology) contains no torsion for $i>0$ for every compact subset $X$ of $\Bbb R^3$.

It is obvious that "Cech homology" contains no torsion (even for a noncompact subset $X$ of $\Bbb R^3$), because it is the inverse limit of the homology groups of polyhedral neighborhoods of $X$ in $\Bbb R^3$. But I don't think this is to be taken seriously, because "Cech homology" is not a homology theory (it does not satisfy the exact sequence of pair). The homology theory corresponding to Cech cohomology is Steenrod homology (which consists of "Cech homology" plus a $\lim^1$-correction term). Some references for Steenrod homology are Steenrod's original paper in Ann. Math. (1940), Milnor's 1961 preprint (published in http://www.maths.ed.ac.uk/~aar/books/novikov1.pdf), Massey's book *Homology and Cohomology Theory. An Approach Based on Alexander-Spanier Cochains*, Bredon's book *Sheaf Theory* (as long as the sheaf is constant and has finitely generated stalks) and this paper http://front.math.ucdavis.edu/math/0812.1407

As for torsion in singular $4$-homology of the Barratt-Milnor example, this is really a question about framed surface links in $S^4$ (see the proof of theorem 1.1 in the linked paper).