In a prior post, Creating the R3 technical environment, I spoke about an element id issue:
"The second issue is element ids - Microsoft added some objects. When we loaded our CUS layer model, we had element id conflicts. Objects that we created in the CUS layer had the same element id as some of the new R3 Microsoft objects. We had to update our objects to a higher unused element id number. We will be creating a powershell script to do this in an automated fashion for future compiles."
It ended up that this was not the solution. When working the layers rather than de-installing and installing models, you install the R3 models with the -replace command. This retains the legacy IDs. Each layer goes through a code upgrade.
So after another go around, we have our R3 Test environment with all custom fields and tables.