Imported the data back into Maya from ipisoft and re-targeted the bones again. This shows the final result. I'm planning to make a video later showing the entire process on how I achieved all this.

After doing the whole workflow, you don't actually need to import your character into ipi soft. That is just for you to pre-visualize. Instead I exported that data from ipi soft dummy (in my findings, this is the only data / bone information you can export anyway) as BVH file and converted into FBX in MotionBuilder.

Then I loaded the character with the HumanIK created previously, create a new Character HIK to apply the new data from ipi dmc, change the source of animation and done! It took me a while to figure it out but it's all done now.

I basically described the whole process here. Let me find sometime and do a video tut showing the whole process with my cowboy. However, I won't be going into weight skinning as this will take forever. It took me really long time to get the right weight skinning and now I have to redo it again because of the new movements. But once you understand the whole process, everything is just plug and play. I'm not sure, but looking back, I think what will take the most time to "fix" will indeed be the weight distribution where you don't want parts of the body go inside and out.

ipi Soft to Maya Final Result - YouTube