Do you like particularly like macro photography?
If so, I would say the macro is obviously the way to go.
If you are not stuck on the macro thing, and are going to go with the 5Dii, I would consider the 17-40, which is about $350 more than the 100mm, but I could see it being worht it. The 17-40 would take advantage of the full frame of the 5D more than the 100mm. You already have the 100mm covered with the 24-105, so with the 100mm, you are really just getting the macro capability, and a faster lens at 2.8.
That said, the combo of the 24-105 and the 17-40 would leave you with nothing faster than f/4, but even if you were to go with the 100mm, that would be all you could use for anything faster, and that seems kinda limited. If you want some speed, I would sacrafice the reach of the 24-105 for the 24-70 2.8, but then you are adding to the cost of your whole setup here, and that might push you out of your budget.
I have a 7D, and end up using my old 5D more than that a lot of the time, unless I need high ISO, or am looking for "reach" on the 7D.
There are so many choices, and they are all great. Good luck figuring out what is goin to suit you best. Let us know what you decide.
As for getting your flash off your camera, you can do that pretty cheap. I use vivitar 285's, and cactus triggers. Both pretty cheap. I do have a canon flash that I use on my camera, but you can get an off camera setup pretty cheap, then decide if that is something you will use, then expand on that.
6D, 5D, 20-35 2.8L, 135L, 70-200 2.8IS L, Sigma 50 1.4, Sigma 105 2.8 macro, SMC Takumar 28 3.5, SMC Takumar 50 1.4, Super-Takumar 105 2.8