I've been building out the eastern US, working my west.  So far I've been creating links to my custom scenery folder one tile at a time.  Is there a better way to link large amounts of tiles, so that each tile is not an entry in the scenery.ini file?

I don't think so, I have seen this question come up several times and yet to see an answer. xorganizer seems like a popular tool to help you manage it. 

For creating links, you can try Shell extensions. You can make links for 100s of folders with 3 clicks in an instant.

http://schinagl.priv.at/nt/hardlinkshellext/linkshellextension.html

I choose a custom build dir withon Ortho4XP, which then puts all tiles within the same Earth Nav Dat folder, so there is only one entry in the ini for all my orthos. You can of course choose separate custom build dirs per region, if you like.