The zero response in Y and Z were due to insufficient number of modes considered. If you take out the CUT OFF MODE SHAPE command, you would see participation in Y and Z. Also you need to include the masses in the Z direction. Provide all seismic masses as part of the first seismic case (case 4 ). Mass definitions in subsequent dynamic cases are not read by STAAD.Pro
From the dimensions of the structure and the cross sectional properties of the members, it is evident that it is not a building structure. IBC Equivalent Lateral Load analysis that STAAD carries out, is applicable for building structures and hence is not appropriate in this case. A generic response spectrum analysis would be more appropriate.
The analysis you have carried out is a linear one and hence the REPEAT load would yield the same result as a LOAD COMBINATION.