I am looking at two upgrade options, give me your thoughts on what you would do. I currently have one body, a 40d, which has served me well. Lenses: 28-135, 100 macro, 100-400L, 70-200L II. I do a wide variety of outdoor photography, landscapes, wildlife, birds, flowers, and macro shots. I do no "people" work of any sort. I am ready to uprade and here are the options I am considering.
1. Get a 5d Mk III with the kit 24-105L and keep my 40d as well.
2. Get a 5d Mk II with the kit 24-105 and a 7d body, sell my 40d.
I can do either of these for about the same amount of money right now.
I forgot to mention that I would be selling the 28-135 in both of these scenarios.
5D3 is a better camera. However, if you compare your 40D image with a cropped 5D3 image (8.5 megapixel ~3570x2380), there may be no reason for keeping 40D.

I assume that you are not a professional photographer and in that case (probably) there is no need for more than 1 DSLR body. If the only reason for 2 bodies is that you want to have both FF and 1.6x crop options, then you have to decide which sensor size is more important for you. You can do everything with just 7D or 5D3 alone. 5D3 has better AF and image quality, but you will need bigger/heavier and more expensive lenses to match the reach of 1.6x crop. If your plan is to use 40D for telephoto and 5D3 for landscapes, flowers or macro (things that do not require top tier AF system or done better using manual focus), then it's hard to justify buying 5D3 over 5D2.
I noticed that your widest lens on 40D is 28-135mm, so if you won't be using any UWA lenses, then 1D4 may be the camera for you.