How can I merge two similar-but-not identical folders?

You can open Terminal and use one of the following (rsync would probably be the one for you if you want something that won't be completely lost if you halt the process):

The standard UNIX way

cp -R -v source/. destination

The geeky UNIX way (restartable)

rsync -vaEW source/ destination

The OSX "easy" way

ditto -V source destination

Source

If you use FileMerge from the Developer Tools on the two directory trees, you will be able to see which individual files have copied as it will do a diff between them and show the differences.

Otherwise rsync might be a bit more automated as mentioned above by cksum.