I use generally the same method as Wayne, although I remove the wheels, side rods and valve gear as a unit. These also go for a
quick dunk in the lacquer thinner, and then get worked-over with a toothbrush. If the gears are all-metal, I also clean them with lacquer thinner and the brush. Plastic, nylon, or composite gears are cleaned with methyl hydrate. Make diagrams, where necessary, to aid in re-assembly.
After all of the parts have been stripped, re-assemble the running gear (minus the motor and worm) and test its rolling qualities. The chassis should roll easily on a sheet of glass - if it doesn't, the time to locate and correct any binds is
before you start painting.
I also like to add a power wire from the tender to the motor, as the electrical connection through the drawbar, especially on older locos, is not reliable due to wear.
You
can paint the frame and running gear without disassembling again, but I usually prefer to paint the frame separately, then add the drivers, rods and valve gear. I prefer to brush-paint the backs of the rods and valve gear and the spoked areas of any wheels, then follow-up with the airbrush. I don't lube the loco at all before painting, as the lubricants will spread too much onto areas that need to be painted. As soon as the paint is dry to the touch, I roll the chassis across the glass a few times (this removes the still-soft paint from any wear points), then lube all sliding and rotating joints. Use a small brush and some thinner to clean areas such as the crosshead guides, but only on their wear surfaces. Don't waste time trying to mask wheel treads before painting - it's faster and easier, after the paint has fully cured, to use a small brush dipped in lacquer thinner to clean them. The drivers are especially easy to do with the loco upside-down and power applied to the motor.
Many painters like to bake the finish in the oven, although you must use a thermometer to ensure that it doesn't get too hot.

And, of course, no plastic parts for this step.

I've never attempted that, although I've also heard that a couple of hours in a suitable enclosure using a 100 watt bulb will work just as well, with less risk of spontaneous dis-assembly. I'll give it a try on my next paint job.
Wayne