1999 flht, trouble sifting from first to second and through the gears, with bike off, shifts fine.

 

I would start with a proper clutch adjustment and see if the shifting improves.

 

The internal clutch adjustment is the first thing to check. It may also be time for a new clutch depending on your mileage. 1999 is a while ago. At about 120,000 miles my stock clutch basket was totally shot. The slots in the clutch basket were so worn and saw toothed that the clutch plates did not slide freely when the clutch was disengaged regardless of the clutch adjustment. This caused the exact same problem you are describing.
I replaced the entire clutch assembly with a Rivera Primo Unit.