Download the paintkit for the aircraft, delete all layers except the wireframe layer of the model. Using the wireframe layer as a reference, start with a base color, make a layer for panel lines, make a layer for rivets, make a layer to shade parts, make a layer for decals and other stuff, export in a MSFS-compatible format, done.
If you do not have a paintkit with a wireframe layer for the model: Create a temporary repaint, load the model file into ModelConverterX, then select the temporary repaint to show it on the model. Load the texture from the temporary repaint that you want to edit into Photoshop or GIMP or whatever and use trial & error to determine the outline of the part on the texture. You can do this by painting a few crosses or dots onto part's texture, export the texture from the paint program and reload the temporary repaint in ModelConverterX. See where the crosses and dots end up on the part and move them to a new location until they are barely visible on the part's edge. Repeat this process with more crosses or dots until you have rough outline of the part on the texture file. Then start creating a new texture for the part as outlined in the first paragraph.
This is the summarized process assuming that you at least know how to create repaints for MSFS aircraft. If you do not, I suggest trying to repaint a few aircraft first before attempting to create new textures from scratch.