I got it working with MO2. In fact MO2 is my preferred way to do things like this.
Here's the workflow:
1) Create a new profile
2) In this profile, activate only the mods you intend to merge.
3) Install Merge Plugins to an easy to access folder.
4) Select <Edit> in the drop down list next to the Run button.
5) Press the + button to add an executable
6) Fill in the Title, and press the "..." button and navigate to the Merge Plugins install folder and select the executable.
7) Click OK, then select Merge Plugins from that drop down list, and press Run.
Then just follow the instructions on the Nexus page for using Merge Plugins.