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The automatic merging of different edge count/flow parts is one of the things that make Fuse so cool. Fuse actually started as a Stanford research project tackling this complicated problem.
We do have features planned for blendshapes and user-created imports, but it will take time for the R+D and implementation. For now, major props on delving head-first into Maya (she's a fickle one, but I couldn't live without her)!
And yeah, Maya is a pretty amazing program. And it's clearly one of those "gets better the more you use it" programs. Every new thing I learn in there makes me feel like I'm accomplishing something. If I can figure out a decent process that doesn't take TOO long, for sticking custom heads, onto the Fuse bodies, I'll be golden. And if a future Fuse version can somehow let us import our own heads, and have it automatically lock everything in place, without making us worry about edge counts, that would be a dream come true for me. I'm not 100% sure if that's what you're saying it could (potentially) do, but if that's the case... AWESOME! I can't wait for whatever features are added once an update is released.
To be honest, I don't know if I really need to join it or not. My end goal is to put the model in Unity, and when I do that right now (chop the head off the Fuse model, position my custom head in place, don't worry about attaching it, but link it to the head bone or whatever so that it'll rotate, etc...) Then when I import it into Fuse, the arms disappear, and my head shoots 2 feet or so above the rest of the body (with nothing linking the two). So I figured maybe if I had those "properly attached" then it would fix the issue, but it could be something as simple as deleting the history of SOMETHING. I just don't want to delete the wrong thing on my head mesh, and end up losing all of my blendshapes. And I don't want to delete anything on the body that would cause it to no longer be synced with the Mixamo rig, because I'd rather not have to re-weight everything, and reattach everything (defeating the purpose of the Mixamo rig in the first place).
My character design is basically just a basic Fuse model (with a T-Shirt) so the head is sticking out of the top of the T-Shirt, and my custom head doesn't have MUCH of a neck (think of it as stopping right around where the Adam's apple would be or whatever). So I was wanting to basically use the shoulders/lower neck of the Fuse model, and connect my head with that. (Which is why I ddn't just remove the entire Fuse neck, keeping ONLY the arms), because I still need part of the Fuse neck for what I'm trying to do. And I don't REALLY want to add any crazy clothing or whatever else around the neck, because a guy with a T-Shirt walking down the street with a thick scarf would look really weird.
To be honest, FOR NOW, I don't care THAT much about having "a little bit of a seam" there though. All that I really want, is to be able to import the character, with the full body Fuse/Mixamo rig, and my custom head, without it popping off the character and floating above the body. I'm sure I'm just missing some sort of simple history step or something somewhere along the lines, if you guys are saying I shouldn't HAVE to attach all of the edges.
I was also under the impression that you can't have "holes" in your characters or something though, if importing them into Unity. (I could be thinking about a rule I read for some other software somewhere though). But I was under the impression that (as an example) if your arms go inside a T-Shirt, but are technically missing polygons on the inside where you can't see it, then that would screw something up. It's very likely I misunderstood that rule though.
I'm not familiar with Unity, but I do know the kind of things that go wrong in Blender. Head jumping up 2 feet sounds like an unapplied transform on the head part of the mesh. When you bring it in to your modeling tool, in Blender I would be sure to apply location, rotation and scale transforms. Location should be 0,0,0. Rotation should be 0,0,0. Scale should be 1,1,1. Hopefully you can translate this thought into the Maya equivalent.
Sadly I don't have a suggestion for the disappearing arms, unless they are disappearing into the body, in which case it's to do with the bone hierarchy at the shoulder and the rest pose.
I am having to edit the Mixamo skeleton to match the number of bones and bone hierarchy for my platform (Ogre). When I use Makehuman instead of Fuse, I also have to convert the rest pose from A pose to T pose.
But now the only question I have at the moment is... One final error (warning) exporting from Maya... Does this mean anything to anybody? I'm ASSUMING it's one of those warnings I can just ignore, and assume it won't mess up anything since it says "to ensure interoperability"... But still, I've come this far, I'd like to be able to knock out any final warnings if they're relatively easy to fix.
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Warning: Animation curve tangent type changed to User (159)
The plug-in has changed some animation curves tangents type to User to ensure interoperability. This mode change will not affect the animation curves' values
Hips_translateX
etc...
While you are super close to your result, I'd encourage you to try out a simple blendshape in Unity test with a cube or something. The blendshape system is new and could use a little improvement, but its pretty straightforward and easy to use (blendshape keys exported from Maya play from an FBX just fine, but having joints and blendshapes together had some issues). What we've done at Mixamo for our Unity Blendshapes on faces is to keep the body joint and facial blendshape animations as separate fbx files and add them together with a very simple mechanim setup.
As for the blendshapes, my main reason for skipping that for now is, when I imported my character into Unity, ALL of the blendshapes for the head, were stuck to my characters back like a back pack. I didn't want them all to be visible obviously, since they should JUST effect the main head mesh. So instead of leaving thousands of additional polygons of overlapping faces stuck to my character'a back for no apparent reason, I just deleted them for now.
I still have a copy WITH the blendshapes though. Any idea where I went wrong with the export/import here? Something that would cause all the blendshape heads to be stuck to your character's back in Unity? (I got the main head positioned properly, but even when I tried to move all of the blendshapes into the exact same transform position as the main head, you could still see ALL of them when the game started, which basically just made my head look thick, distorted, overlapped, etc...