For the implementation of a longitudinal design you can just copy the question group and use the expression manager (relevance equation of the group) to show or hide the group according to a condition of your choice (set a hidden field using the assignment operator, don't show before/after a specific date, show/hide depending on a token attribute you can set, etc.). This way you can use one token table and you have all the answers to previous questions available (the group they're in is just hidden).
So you can copy the answers easily using the assignment operator: create a question of the "equation" type at the end of the group which pre-sets the answers of the questions in the same group ({G2Q1 = G1Q1}{G2Q2 = G1Q2} or something like {G2Q3_SQ1 = G1Q3_SQ1}{G2Q4_SQ1 = G1Q4_SQ1} for subquestions like multiple choice boxes ...).
Edit: you might want to set some conditions (if) for the assignment operation or the changed answers will be overritten ...
For this to work you need to set the corresponding token settings in the survey: allow multiple responses ..., Enable response persistence ..., Don't set cookie to prevent repeated participation ... In addition to that you need to set the $deletenonvalues variable in the /application/config/config-defaults.php file to 0, otherwise your previous answers will be deleted.
At least this is the approach I adopting (without the pre-setting of the answers though, so no guarantee for that) and it works pretty fine so far. What I'm not so sure about and what would be interesting are the security issues. Are the questions and answers in a hidden question group written in the source code of the page? Maybe someone of the developpers could answer this question ...
Greetings