Hi Jacob,
I suspect lag because I've worked on databases with millions of rows and haven't had any issues with linking the tables.
Something you can try, is have Crystal limit the number of database objects it lists. This is done in the Settings window. When the Database Expert opens a table, it goes out and grabs the metadata for that database object so it can map it. If it looks like the Database Expert is taking a long time to retrieve objects and link, limiting the number of objects it sees may help.
Good luck,
Brian