[LS short box]

Andrew over on LS1tech is very good on the Holley stuff. He does online tuning via I think Team Viewer.
I kind of curious why your tuner converted to speed density. Typically its done for turbo type engines.
I've done a number of LS swaps using GM ECM's and mass air. My tuners had no issues getting the tune spot on.
Nothing against Holley. Good luck with your project.