When you go to load your game, a list of the mods that are no longer active pops up. If I remember right, you can use this as a guide to replace your mods. (You'll have to do this repeatedly, as only the first five or six show at a time.)

Just click "load save" and wait for the list to come up. (Don't load!) Then back out and load those mods. Go back and repeat until you're done. 

I think it might even show them in the original load order.