Hopefully I'm not over simplifying what your're trying to do...
Maybe try the Fit Model Platform?
Include Group, Var1, Var2, Covariate, as effects. (not sure what the Response (Y)) is in this example.
Use the Effect Leverage option for Emphasis (makes the next step easier)
In the report, click on the red triangle menu in the leverage plot for Group (top row of graphs in the report)
you can display the least squares means plot and also the least squares means differences students's t.
JMP Systems Engineer, Health and Life Sciences (Pharma)