(1) Unfortunately, we don't have many references, aside from the tutorials and Chemkin theory documentation. The most direct way to get an understanding of how the module works is to go through the tutorial and try to understand how the contents of the mechanism relate to the various Chemkin inputs. (Most Chemkin mechanism files are just text files, although some are encrypted.) The Chemkin theory manual has a section on plasman systems that will show what calculations are going on behind the scenes.
The difference between a Plasma PFR and a regular PFR are the inputs relating to plasma and electrons. These inputs, (and the associated reactions) affect how the CH4 reactions progress because the information you enter feeds back to the chemistry calculations. If you double-click the C1_Plasma_PFR in the tutorial, you will see these inputs. Mouse-hovering over the text that describes each entry will pop up a description of what it is, so that you can relate it back to the nomenclature used your own studies and any papers you use as background.
(2) For the thermal and microwave plasma driven pyrolysis of methane (see the two links), people have been combining the gas phase mechanism for methane (combustion chemistry) with a bunch of reactions involving excited species (plasma initiation). You may need to do a bit of digging to come up with the best reaction set for plasma initiation
Pressure in the plasma driven process is much higher than that in a stabilized plasma process (e.g. CVD). Therefore, many users are simply ignoring the separate electronic energy equation and related adjustment to the bulk gas energy equation that is described in the Chemkin Theory Manual - Ch. 8. With that simplification, excited species in methane pyrolysis are treated like other gas phase radicals. The process is driven by the reactions and rate constants in the mechanism.
The Chemkin Inputs manual describes the reaction mechanism syntax and elements of mechanisms. The reference below, which I found on the web with a search on :"Ar plasma reaction", provides a lead to several other papers, specifically Reference (3) that claim to present mechanisms suitable for modelling:
One of these could be combined with the Grimech 3.0 combustion mechanism for methane.
(3) The dispersed (particle) capability in Chemkin is activated by keywords in the Chemkin mechanism file. Including a DISPERSED material in your Chemkin mechanism will allow Chemkin to recognize particles in a simulation, and is another way of introducing a reactant. With this, you usually would also declare a corresponding bulk specie that participates in reaction. The mechanism from the tutorial "closed homogeneous particle aggregation" with dispersed phase TiOX is a good example to look at to see how a dispersed material interacts with chemistry. A full description of DISPERSED phase materials is given in Chapter 6 of the Chemkin Inputs manual.
(4) To adjust the Soot Formation and Growth in a JSR/PFR Reactor tutorial for CH4, load it and then Edit the Chemistry set under Preprocessing, You will replace chem_abf_1bar.inp with a revised gas phase mechanism that is tuned for CH4 oxidation. (If you edit the file chem_abf_1bar.inp, you will see that the C1 C2 chemistry is borrowed from Grimech 1.2, which is just an older version of the more recent Grimech 3.0 mechanism, so some reactions may overlap.) Replacing chem_abf_1bar.inp with the Grimech 3.0 mechanism file, grimech30_chem.dat in C:\Program Files\ANSYS Inc\v19x\reaction\data will take care of the methane chemistry. Then, run the Preprocessing to check if your Thermodynamics data file will need any additional species. You can edit the existing therm.dat file and add these by copying from the Grimech 3.0 thermo file grimech30_thermo.dat in C:\Program Files\ANSYS Inc\v19x\reaction\data