Hmm... interesting thoughts. We don't really talk about/have commands when riding the tandem. About the only thing I ask (as captain) is whether he is ready when we're at a full stop and we're getting ready to start again, just to make sure (sometimes he's not paying attention and we both dismount at stops - which works for us - so need to be sure we're both ready to mount/pedal... if I don't get some sort of "okay" or "yes" I don't go). That is about it except for warning about big bumps or coasting (which we don't do very often unless down a mountain side and we're out of gears). Occasionally, I'll ask him to signal a turn, but usually he just does this on his own.
Really, we took to tandem riding pretty fluidly, even from the first ride (despite my being completely unnerved about being responsible for both of us - which I still take seriously, but don't feel the tension I felt early-on now). I'd read so many horror stories for years before starting to actually ride a tandem (which is why we didn't start sooner - I feared we'd just argue constantly), so I was shocked at how easily we took to it. Haven't had any major fights yet, but it's still fairly new for us at 4-5 years now. Maybe because we've both ridden solo for a long time or because we communicate in everyday life pretty effortlessly anyway? I'm not entirely sure what the reasoning is, but am grateful that it hasn't been a difficult process at all and we haven't had a need to set up many cues/commands.
I can see that for some it may be beneficial to start off with a set of cues to keep both people on the same page, but I also think that there is no universal set of rules that have to be followed. As long as both captain and stoker know what's going on, that's what matters, I think. Perhaps finding out what your stoker is thinking/feeling before creating this written rule book would be beneficial? You said you've been riding a tandem for a long time - is it new for this stoker? Have they ridden solo bikes? Even if not, s/he may have thoughts/fears that would be good to get before creating the list. I know I wouldn't like someone telling me how it's going to be without getting my opinion... but maybe that's just me.