The multi-scheme chemical ionisation inlet 1 (MION1) enables rapid switching between the measurement of atmospheric ions without chemical ionisation and neutral molecules using various atmospheric pressure chemical ionisation methods. In this study, we introduce the upgraded version, the multi-scheme chemical ionisation inlet 2 (MION2). The new design incorporates enhanced ion optics, resulting in increased reagent ion concentration, ensuring a robust operation, and enabling the use of multiple chemical ionisation methods with the same ionisation time. In order to simplify the regular calibration of MION2, we developed an open-source flow reactor chemistry model called MARFORCE. This model enables quantification of the chemical production of sulfuric acid (H2SO4), hypoiodous acid (HOI), and hydroperoxyl radical (HO2). MARFORCE simulates the convection-diffusion-reaction processes occurring within typical cylindrical flow reactors with uniform inner diameters. The model also includes options to simulate chemical processes in the following two scenarios: (1) when two flow reactors with different inner diameters are connected and (2) when two flows are merged into one using a Y-shaped tee, although with reduced accuracy. Furthermore, the chemical mechanism files in the model are compatible with the widely used Master Chemical Mechanism (MCM), allowing for future adaptation to simulate other chemical processes in flow reactors. Furthermore, we conducted a comprehensive characterisation of the bromide (Br-) and nitrate (NO3-) chemical ionisation methods with different ionisation times. We performed calibration experiments for H2SO4, HOI, and HO2 by combining gas kinetic experiments with the MARFORCE model. The evaluation of sulfur dioxide (SO2), water (H2O), and molecular iodine (I2) involved dilution experiments from a gas cylinder (SO2), dew point mirror measurements (H2O), and a derivatisation approach combined with a high-performance liquid chromatography quantification (I2), respectively. Our findings indicate that the detection limit is inversely correlated with the fragmentation enthalpy of the analyte-reagent ion (Br-) cluster. In other words, stronger binding (resulting in a larger fragmentation enthalpy) leads to a lower detection limit. Additionally, a moderately longer ionisation time enhances the detection sensitivity, thereby reducing the detection limit. For instance, when using the Br- chemical ionisation method with a 300 ms ionisation time, the estimated detection limit for H2SO4 is 2.9×104 molec. cm-3. Notably, this detection limit is even superior to that achieved by the widely used Eisele-type chemical ionisation inlet (7.6×104 molec. cm-3), as revealed by direct comparisons. While the NO3- chemical ionisation method remains stable in the presence of high humidity, we have observed that the Br- chemical ionisation method (Br - MION2) is significantly affected by the air water content. Higher levels of air water lead to reduced sensitivity for HO2 and SO2 under the examined conditions. However, we have found that a sharp decline in sensitivity for H2SO4, HOI, and I2 occurs only when the dew point exceeds 0.5-10.5 °C (equivalent to 20 %-40 % RH; calculated at 25 °C throughout this paper). For future studies utilising the atmospheric pressure Br- chemical ionisation method, including Br - MION2, it is crucial to carefully consider the molecular-level effects of humidity. By combining approaches such as the water-insensitive NO3 - MION2 with Br - MION2, MION2 can offer more comprehensive insights into atmospheric composition than what can be achieved by either method alone. By employing instrument voltage scanning, chemical kinetic experiments, and quantum chemical calculations, we have conclusively established that the presence of iodine oxides does not interfere with the detection of HIO3. Our comprehensive analysis reveals that the ions IO3-, HIO3.NO3-, and HIO3.Br-, which are detected using the Br- and NO3- chemical ionisation methods, are primarily, if not exclusively, generated from gaseous HIO3 molecules within atmospherically relevant conditions.