I have tried making a script to generate the motor6D motors that act as the joints for the model, based off the dummy rig... but can't get the plugin to recognize it.... I am sure some/most of this script is wrong but here is a snippet of what I did.
r = Instance.new("Motor6D", workspace.Monster.HumanoidRootPart)
r.Name = "Root"
r.Part0 = workspace.Monster.HumanoidRootPart
r.Part1 = workspace.Monster.Torso
r.C0 = CFrame.new(0,0,0) --I know the numbers here aren't correct.
r.C1 = CFrame.new(0,0,0) -- and here.
Solved it by using the Character Creator Plugin and the AnimRig2 plugin. Things the model needs is
-HumanoidRootPart (this is like an invisible torso) Note this part needs to be anchored.
- -Torso(Is linked to the HumanoidRootPart via Motor6D created by the plugins) ---Head(linked to torso via motor6d) ---other parts like arms, legs...(linked to torso via motor6d) Note: all of the surfaces on the parts making up the model need to be smooth and not anchored (except humaniodrootpart needs to be anchored).

3 comments
Try naming it RootJoint instead?
You need to make sure everything is where it should be; http://wiki.roblox.com/index.php?title=Animations#Animating_Custom_Models
So I have those things and I can select it in the animator, but when I try and rotate part of my model shoots up super high in the sky.