No, Weber jets don't work in Dellortos. I don't know about Mikunis. I know you can use Weber jets in OERs, though. OERs are also cool because they have externally-adjustable float level and accelerator pump, and they're boost-prepped from the factory. If I were to buy a new sidedraft today, it'd probably be an OER.
Nope, can't mod a sidedraft to be a downdraft. The float bowl would be in the wrong position. You could use it as a downdraft EFI throttle body, though. The bolt pattern and bore spacing are different, too, so it'd have to be a custom manifold.
No, twin 40s sounds like a great idea to me. On eBay recently there was a twin IDF manifold for a 4-port 13B. I wanted it so badly.
What kind of ports are you going to be running? If peripheral ports, one of the big Gene Berg IDAs would probably be your best bet. For side ports, might I suggest twin 45mm OERs/DCOEs? This is assuming you can make your own intake manifolds, of course.