Sorry if that's confusing... this is one of those 'easier than it sounds' types of things.
If you've made it that far, you have on file with all of your left hand pages, and one file with all of your right hand pages.
Open the file that contains the first page (should be the left-hand-pages document, "File #1").
Make sure you have the Sidebar open ("View/Sidebar"; Cmd-Shift-D; or the "Sidebar" button in the top toolbar). In the bottom of the sidebar, there should be button with two little boxes beside two little lines. Click that, and choose "Thumbnails" from the three options. (This will ONLY WORK if you have the thumbnail view selected— I may not have made that clear enough last time.) The sidebar should now show scaled down previews of each page, laid out in a grid. (See the first attached image for how it should look.)
Now open your other file (right-hand pages, File #2) and set it up the same way, with thumbnail views. In File #2, the first page in it should be the second page of what will eventually be your finished document. Click and hold the thumbnail of the first page in File #2, then drag it over and drop it next to the thumbnail of the first page in File #1. A little red bar should appear to show where the page will be dropped. (See the 2nd attached image)
Now comes the tedious part of dragging each right hand page from File #2 to the correct place in File #1, making sure all your page numbers end up in order. Once you've done that, just Save!
Just lemme know if you need any more clarification.
Last edited by senseabove; 02-03-2009 at 07:26 PM.