Connecting to SIM800L

you would just maybe issue a wait or a SetTimeout for the AT+BAR command to ensure all of the AT+FOO response lines have been either handled or flushed?

I'd handle all 3 lines - adding a timeout would work, but it's pretty nasty and might bite you later on. It's not hard - at the most basic level:

at.cmd("AT+FOO", 1000, function (first) {
  return function(second) {
   return function(third) {
    // done
  };
  };
});

Or you could actually count the lines - but in a lot of cases there's an OK message or something to signify the end of the response that you can use:

at.cmd("AT+FOO", 1000, function cb(d) {
  // stuff...
  if (d!="OK") return cb;
});

I guess though that can't happen because you don't know what response from the modem is tied to what command...

Exactly - it's really the responsibility of the at.cmd's callback to keep track of the response that it is expecting.

I may just go ahead and tackle a rewrite on the SIM900 module.

Is the existing one not working for you? It sounded a lot like after the wiring issues, it was working ok?