checking prices at B+H, the 5D w24-105L is more expensive then a 5D w/an MPE-65 by about $100. Id get the 5D w/the MPE 65, sell the Canon 100 Macro and pick up a Tamron 28-75 2.8, should give you a Phenominal macro lens, and a pretty good lens for portraits and its just about as wide as the 18-55 is on the 350D, so it should work for landscapes as well. Or sell the 350D and 100 Macro and pick up a 17-40L.
I do think the 40D might work better for Macro with the Live View feature and the MPE being Manual Focus Only. One option would be get the 40D, MPE 65 and 10-22, then maybe something to pickup up something to cover the gap between 22 and 70 (Sigma 24-70 perhaps)
5D - $2499
5D w/24-105 - $3400
5D w/MPE 65 - $3328
5D w/MPE 65 and the Tammy - $3697
40D - $1299
40D w/MPE, 24-70, 10-22 - $3246
Heck, you could even replace the Sigma with a Ring Flash. Or add a ringflash and be about the same as the 5D with MPE and Tammy.
Honestly, Id lean more towards the 40D, but you will need a flash with the MPE 65
prices are from BH
-Johnny