Welcome back!
-Learning 3D modelling software is a science on its own, but here whatever package will do so long as it can export .OBJ format, from this point, you run a GLBasic tool called OBJ to DDD or something like that and convert your object to its native format. I think you can have one UVmap attached to it, a color texture and a bump map texture. It is said to be always better to use a texture to color polygons but who knows. It can also convert a sequence of objects, say you have a modeled monster, then you shape a walking pose and save as 001 anther pose and 002, etc. You can access these as animation key frames and can blend through it. I particularly use Lightwave 3d for modelling because of my work, it is an expensive tool and I can´t remember if the demo will do. Blender is great but it is easier to learn machine language for 512bits processors, Sketch up is more or less free and has a neat simple modeling tool, there are also plenty of online 3d modelers.
-There is no plan to support Pyra but I think it should not be a hard deed to do so. Let´s raise the subject when some machines start hitting the crowd for there may be more people interested into such. As far as I tested and ported my 2d games to Pandora, it worked fine, it was just that I had to do some version shuffling. Some one was developing a game called Reggie´s World, I think, and it is a 3d mario/zelda styled one. Runs great on the pandora. If Pyra gets any layer of compatibility with the pandora, then there is already one path to develop for it.