Assuming an easier solution doesn't present itself before the transition is finished, please consider the following:
-All threads will be relocated to the new forum, therefore there will be a post by all members who have a post count = 1+
-I have made a list of all current members who have a post count above 0, in descending order of postcount (this is mostly so shyts organized)
-I suggest that if everyone wants rep to be restored, once we settle into the new site we make a rep boosting thread; starting either at the top or bottom of the list (I mention starting from the bottom as the users with highest postcount tend to have higher rep values, not always but y'know. Therefore the people who benefit most need to wait til the end to restore their rep) and posting that users final rep from here, along with a link to a post of theirs on the new boards.
Everyone else in the thread/from the old site then uses their upreps throughout the day on that post, etc. etc. until everyones got their stats back.
One rather large thing to consider is whether you are prepared to invest the time to do this; as someone has advised me already, if people get bored halfway through it breaks the system and is unfair on some people.
Also, you will have to trust (and in turn do so yourself) that everyone helps out everyone else. Again this system will breakdown if they only help people they like...
So yeah, word...
EDIT: also you know, critique/improve/tear this idea apart til you come up with something satisfactory for everyone.