Derek:
Sorry about your problem, I don't know if you will be able to find a DNN specific tool to compare the two sites and copy the differences like you need. You may want to search in www.snowcovered.com to see what's offered. What you want to do is very tricky, even if both sites are the same, the fact that tabs, modules, and other structures were not created exactly the same way will cause the problem of having different ID numbers, even if both sites look and work exactly the same way. Trying to match these objects' ID numbers could be very difficult if not impossible depending on the number of instances you have.
That said, what version of DNN are you using? If it is one of the newer versions you may try the per module Export-Import functionality. Be careful testing this, make sure you have a good backup before you start importing.
Also, since it sounds urgent enough, you may want to look at the tools by Red Gate at www.red-gate.com. Specifically they have "SQL Compare" and "SQL Data Compare" to compare and synchronize just structures or structures and data respectively. They are not cheap but you have to weigh their cost against the labor of doing the work by hand.
Sorry I (or someone else) don't have a better answer.
Good luck and let us know what happened.
Carlos