Of course, I'll begin with the standard disclaimer that your SM should check with the AEA rep. I humbly offer my interpretation, based on my rep experiences.
Do we have to limit the rehearsal hours of the folks involved in both shows per the rule that says there can only be 5 1/2 hours of rehearsal on a one show day?
Yes. Actors rehearsing and performing at the same time may only be rehearsed up to 5 1/2 hours, on a one show day, providing, as you say they did, they voted against the two hour call on one of two, two- show days.
*Related to that: If we do have to limit our day to that 5 1/2 hours worth of call, does it have to be consecutive or can there be a meal break in the middle (we were originally going to do a full day, and the director has an newspaper interview during this already scheduled break)?
You only have to limit the actors who are both rehearsing/performing at the same time. The rest of the company not in performance may be rehearsed according to your theatre's span of day preference 7/9, 8/10, etc. You could schedule a straight-six, providing that the company voted to rehearse such a day and the rep actors are only called for 5 1/2 hours of the six hour call. Your director might be able to do the interview on the 20 minute break. Breaking up a 5 1/2 hour call with an hour or hour and a half break would be counter-productive and would most likely violate the span of day rule for the rep actors, which I believe is 12 hours.
*Also: How does this affect our span of day? Does the day for the overlapping actors need to be calculated from beginning of our rehearsal to the end of their performance for the other show?
Yes. You must also be careful not to violate the 12 hour rest period, unless they have requested and voted to reduce it to 10 on one performance days.
Don't forget about the daylight day of rest for those rep actors, too.