I asked my peers about pausing and resuming a print cleanly. They recommended editing the G-Code.
Inserting the Gcode into the file
After slicing, use the Paths view, and raise the vertical height slider (immediately to the right of the main view) to find the height at which you want to begin the new color.
Save the GCODE output file, and open it with Notepad or some other text editor (Scite is free).
Find a line like this, where the Z value is just under the height you want to start the new color: END_LAYER_OBJECT z=6.00
Insert this section of Gcode, which works with Pronterface:
If using Pronterface: (for Octoprint or Repetier, the inserted code is different - see below)
G28 X0; move head out of way (will preserve feedrate)
M117 — Insert Bearings now —
M0 ; pause the print - waits for open and close of filament switch
G28 X0 ; fix up in case head got moved while changing filament
It should be before a few lines like this:
; Reset extruder pos
; BEGIN_LAYER_OBJECT z=6.25
the Z value there should be the value you want to start the new color with.
Message to the User
The M117 command will echo whatever follows it on that line, to the log window. Use it to indicate what the pause is for.
M117 Change to BLUE
M117 !!! Change Color !!!
M117 Put In whatever color you like
M117 Insert Coin