The electronics in that engine are probably the TAS "SAW Board." SAW stands for Sunset, Atlas, Weaver because TAS was supplying those boards to the Lionel licensees. I don't know about the Cruise Commanders kits, never installed one, but I seem to remember that TAS made an EOB drop-in kit that would work with the SAW board. Of course, those kits aren't exactly easy to find these days. I have a couple laying around somewhere; if I can find them I will check the instructions to see if they would work with the system on the S-3. Or, you could check with Weaver - Gary did a lot of TAS upgrades on Weaver brass engines before the TAS boards became unavailable.
The S3 was one of a very few Weaver engines to have the TAS puff and chuff synchronized smoke system. I can't remember if mine has two or four chuffs per rev; it's been over a year since I ran it.