Charles, You are in exactly the same place as I am right now.
I have the plane elevated (sans engine) and AM working on the fairings and wheelpants because the fuse is easier to lift and orient in a flight attitude without the 300 lbs of engine hindering the process.
I will take the plastic stuff off and store them until after the first flight just to keep them from being in the way.
You are right. No need to have them installed now but there will never be a better time to fit them than the present.

CJ