You can't get answers for questions like that in a forum like this. It's likely to be a huge project which will take months of analysis, risk mitigation, functional testing etc. If you need to ask "how to do it" on a forum then you need to get some knowledgeable people into your organization quickly. Good luck.
There are two ways to do this.
1. Decide on which existing instance will be your target instance, or create a new one, hire or train a bunch of developers to extract all the data you want to import from the source instances and use the public APIs to convert/import the data into the target instance.
2. Purchase Eprentise EBS Instance Consolidation software to do this for you.
I have done this type of project. First design the whole org hierarchy. Decide what would be reporting structure, and relationship among the multiple org and LE and SOB. This is very important.
Here is a simple example:
1. Decide one instance, as a base instance
2. Define a common COA (if you want to use org hierarchy in the EBS instance)
3. Define Org hierarchy, security profile, and HR profile
4. Design process mapping and CEMLI migration
5. Data mapping and migration
This is a sample, planning and roadmap are important.