I've repainted quite a few S-2's, so here's some other pointers and tips.
First off as RSJB mentioned, wiring the motors in series does help to slow them down. BUT if you run these with a transformer like the Lionel 1033, using the B-U voltage post setting of 0-11 volts, they WILL run slowly for switching. Most Lionel transformers have a minimal 6-7 volts to start, which is what causes the jack-rabbit starts. As a side note on this point, when RMT reissued the S-2 as their S-4, they used a motor with different specs, so that the RMT S-4 BANG will run slowly even with a normal Lionel transformer.
1) Once you remove the shell, you have the window insert on the cab which usually does not pull out easily. The best way to remove it, is to tap the cab end of the shell (bottom side) against a block of wood. It will eventually loosen up and gradually work it's way out.
I choose not to use the window insert again as it is like a box and not open on the top, allowing access to the rear headlight, should you chose to wire in an actual headlight as I do. More importantly, I also add an actual headlight to the front of the engine, removing the long piece of styrene from the inside of the shell. I use the mini T 1-3/4 type bulb and socket which are available in either 6 or 12 volts. For an engine wired as was, 6 volt works good. If you rewire the motors in series, then a 12 volt is better. I'm sure there are also LED's that would accomplish the task.
So using the plastic from a gallon milk jug, I measure and cut a piece that is long enough to cover just the back and both sides of the cab. I cut very slight perforations into this, where I will fold it so that it looks like an angular "U." This slides in and also out of the cab part of the shell very easily, unlike the included window part.
2) There are 2 different molds for the K-Line S-2. The older one has very deep channels between the side doors of the long engine part of the shell. A later version had these channels filled in, so that the sides were smoother and thus easier to paint. Notice that the early issued K-Line S-2's always had the lettering above these side engine access doors. Compare one of the early issues to one of the later ones like the Frito Lay S-2 and you'll see the difference.
It's interesting that when RMT re-issued the S-2 as their S-4, it was with the earlier mold with the deep channels between the engine access doors, albeit with other alterations such as the cut out rear cab door window and door handrails added, along with the different type of smoke stack. Obviously the painting/lettering technology has improved to allow better painting over these side hood door channels.
When I've repainted the earlier engine shells, I often use thin strips of styrene, glued into those channels between the access doors, so that it makes painting and decaling the shell much easier.
3) With the hand rails, I've done one of two methods. With both I fill in that hole in the cab for the handrails. The way it is now makes it easier to get paint scratches in the future. Then I either shorten the handrail just a little bit and put a piece of plastic wire insultation (pulling the stranded wire out) from black wire, and place that over the ends of the handrails.
The other method is to cut the entire end section of the handrail off, right after the last handrail station. I've found you can stiffen up the handrail stations by first removing them entirely. Then at the bottom of the stations that insert into the engine frame, I alternative bend one slightly up and the next one slightly down and so on. When you put these back into the engine, it creates a little more tension on the handrails and helps to keep them not as loose fitting.