Slicer settings are pretty important to make the best light pipe you can.

Basically, print hot, decently fast, 5-10% over-extruded, and try to keep the extrusion path linear in the direction of the light pipe.  This boils down to:

• Quality
  • 0.4mm Nozzle
  • 0.2mm Layer Height
  • 0.2mm Initial Layer Height
• Shell
  • 2 Walls
  • 1 Top Layer
  • 1 Bottom Layer
  • Top/Bottom Pattern: Lines
  • Compensate Wall Overlaps: Checked
• Infill
  • Infill Density: 100%
  • Infill Pattern: Concentric
• Material
  • 250C Printing Temperature (yes, this is really, really hot for PLA).  I went as hot as I could without it turning yellow.  Still, if you stop the print and don't shut off the hotend at this temp, you will yellow/start to cook it anyway.
  • 50C Build Plate Temperature (yes, this is hot for PLA)
• Speed
  • Print cooling on, but low until you hit the leaf area.  Then high.
  • Print decently fast.  I used 45mm/sec.
• Travel
  • Combing Mode: All
    • Avoid Printed Parts when Traveling: Unchecked
• Build Plate Adhesion
  •  Build Plate Adhesion Type: Skirt (I have areas added into the model for adhesion)

Use the same settings as you did for the stem, except change this.

• Shell
  • Top/Bottom Pattern: Concentric

This one is a bit strange.  I found using zero walls, top or bottom layers (just infill) worked the best.

• Quality
  • 0.4mm Nozzle
  • 0.1mm Layer Height
  • 0.1mm Initial Layer Height
• Shell
  • 0 Walls
  • 0 Top Layers
  • 0 Bottom Layers
  • Top/Bottom Pattern: doesn't matter.
  • Compensate Wall Overlaps: Checked
• Infill
  • Infill Density: 100%
  • Infill Pattern: Concentric
• Material
  • 265C Printing Temperature (for nylon this is mid range)
  • 80C Build Plate Temperature
• Speed
  • 30mm/sec across the board
• Travel
  • Combing Mode: All
    • Avoid Printed Parts when Traveling: Unchecked
• Build Plate Adhesion
  •  Build Plate Adhesion Type: Skirt 

Got a project log for this:

https://hackaday.io/project/163866/log/160606-forming-the-petals

Normal settings for PLA apply here.  I still recommend using:

• Travel
  • Combing Mode: All
    • Avoid Printed Parts when Traveling: Unchecked