To answer question 1, the more recent patches included new scripting commands that'll allow you to link modules together into one campaign. That should take care of most of the variables you want to carry over. The rest of them you can link to items which you give characters when they exit one module, and which you take away after they enter the next.
With such wonderful technology at your command, it's definately possible to just split it up into various mods that are interconnected.
Most hakpacks will be v1.31 or less. You'll have to wait until someone updates theirs to 1.32 before you can implement them succesfully.
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