So, I've somewhat sloppily put together most of the prototyping before I move on to modelling the 3d prints.
Things I've learned:
The arm hinges are very finnicky. I suspect I'll have to somewhat redesign them once or twice more, but i think I'll have to use a 3d printer for them.
I can hide little feet in the tread gap.
Arm proportions aren't going to be 100% ideal, but this isn't a masterpiece either, so I'm fine with what I've got.
I'm not sure if I'm going to make the canon removable or on a hinge. Hinge means cramming a lot more into a smaller space, so I'm leaning towards a pegged in canon.
The folding panel I've demonstrated in the pic is going to have another fold in it, so the wide piece lines up with the shoulder joints. His head will also flip out from this.
The thermoplastic i use for prototyping is great for that, but i doubt I'd get much use out of it for anything else as it's too flexible. I might use it to cast a megatron head in.
Printing the new parts will probably take a week or more due to a backlog of customers, I'm not quite ready to purchase a machine.
So my next update will probably be posting images of the 3d files before i send them off to print.

 

Saw your question earlier about tolerances in printing. You might pick some brains in the Creative 3d printing thread.

3D Printed Transformers Thread

 

a quick pic of my WIP layout. It took a little while because as I started working on the feet, I realized it wasn't going to work and had to go about a completely different approach. Now that I've got the basic shapes laid out and all the joints lined up, I'm gonna start detailing it out this week after I finish putting the segments into the back piece, and adding the head.
On the plus side, it'll have ankle rockers now.
I think I've decided his shoulder canon is going to just be a weapon on a 5mm port, rather than try to keep it together during transformation.