Separating molecular spin isomers is a challenging task, with potential applications in various fields ranging from astrochemistry to magnetic resonance imaging. A new promising method for spin-isomer separation is magnetic focusing, a method which was shown to be capable of producing a molecular beam of ortho-water. Here, we present results from a modified magnetic focusing apparatus and show that it can be used to separate the spin isomers of acetylene and methane. From the measured focused profiles of the molecular beams and a numerical simulation analysis, we provide estimations for the spin purity and the significantly improved molecular flux obtained with the new setup. Finally, we discuss the spin-relaxation conditions which will be needed to apply this new source for measuring nuclear magnetic resonance signals of a single surface layer.