I did some more fitting and pondering today, while moving and reorganizing stuff in the house so I can actually find things again.
I discovered that the original "good idea" isn't, really, as it would force the seat to be too high and too far forward:
Note taht in the mockup, the motor ends up a couple of inches away from the middle downtube, but in reality it'd be a couple millimeters away, with the headtube/seatpost angle being matched instead of messed up.
So, since there's no way to join the headtube and seattube (for strength) without moving the blue frame down and forward, which then fills the space the motor would be in, it means the motor can't be in the dropouts, and I have to make dropouts for it. Either below the green triangle like this:
or below the blue triangle.
Note that in the latter mockup, the headtube would align directly with the seatpost, so I'd basically cut off the blue frame's headtube and fishmouth the top/downtubes of the blue frame so that I could weld them directly to the back of the seatpost there. Actually just a bit higher, after cutting out the crossbar on teh top of the green triangle.
If I could manage it, I'd ideally like to align the toptube of the blue and green frames, to pass their line straight back and down under the seat, and have the seat mount directly to the top of them. That depends on ground clearances for the stuff along the bottom (pedals, motor, chain) at full bump of the suspension, at it's lowest point of travel (most compressed). Might not be able to, and end up with what you see in the mockup.
If I do manage it, the seat will be tilted back more (which I want), with it's base/back joint still in about the same place it is now. I may have to bend the front edge of the seat downward to clear my legs for pedalling, though.
The square silver rails would be to mount the cargo pods on, and also to provide support for the seat. I'd probably also have to add lower rails like CB2 has, to keep them from hitting the swingarm when loaded, but the lower rails won't have any rear-end support, and will have to extend beyond the rear wheel so I can put a cross-brace on all four rails to keep them spread apart back there under loads.
I also wish the rails could go higher, above the top of the tire, but they can't and still stay inline with the rest of the frame top (which I want), so the pods will not bolt straight across them, but at an angle across the top so the pod tops will clear the tire top thoroughly at full bump, so I can still have cargo up top.
Some pics of the rest of the room, which I've just barely started moving the bike stuff into: