We demonstrate a modified integration of a linear ion trap with a time-of-flight mass spectrometer optimized to enhance the loading and detection of Th3+ ions. A phase-locked radiofrequency/high-voltage switch incorporating zero-crossing triggering and a programmable time delay is a key upgrade to minimize RF phase-dependent jitter and enable the unambiguous identification of Th3+ ions. To enhance purity, yield, and lifetime of trapped Th3+ ions, we optimize the ion loading parameters, including ion trap settings (RF amplitude, endcap voltages, and loading time), laser-ablation pulse energy, helium partial pressure, and ion storage time. These improvements extend trapping lifetimes of Th3+ ions to several hundred seconds, representing an order-of-magnitude increase compared to our previous work. Finally, single-pulse ablation of mixed Sr–Th nitrate targets enables the direct co-loading of Th3+ and 88Sr+ ions, and subsequent laser cooling forms multi-component Coulomb crystals for laser spectroscopy of Th3+ ions. Given the long trapping lifetime of Th3+ ions, this system will serve as a platform for developing a prototype trap-based thorium nuclear clock.