Congratulations, you built your first wheel. It's not perfect, but it will work. You also learned some lessons. As others have said, you could ride as is, or redo it with longer spokes. Nobody will ever know because your error is tucked inside the rim (no "apprentice marks").
Changing the musical tone of a spoke (once you get to that level), is +/- about one revolution of the nipple. You obviously are short by several full turns and should not try to fix this with tensioning. I would call the wheel finished.
Regarding tension tools, remember that for many years they weren't used at all. Double check your tool in every way you can think of. It should be able to repeat a reading, even if the reading is bad, so compare your spokes to the spokes on a known good wheel and see what that looks like. Also a good idea to continue to use the low-tech methods of listening to notes and squeezing pairs of spokes.
Smart idea doing the front first. Good luck on the rear.