Always use at least a minimum of 30% infill, the higher the better.
Print at a slow speed: 20-30mm/sec (1200-1800mm/min for simplify3d).
Extrude at a temperature between: 210-225°C.
Not really needed, but you can have the platform bed temperature set to: 20-50°C.
To reduce stringiness, set retraction for 1.75mm filament, to 2-3mm. Go with the lower amount if using an Ed3. Another option is to turn on the cooling fan.
When switching filaments (ABS or PLA) purge thoroughly before starting a print. Preheat, using a lower temperature 180-200°C.
If you need to glue ninjaflex, 3M trim adhesive and Gorilla Glue provide moderate bonding. The best way to connect NinjaFlex parts is with a hot knife welder.
Lastly, Never, Ever print on PEI, ninjaflex sticks like crazy glue. Use painters tape and make sure to wipe thoroughly with alcohol.
A nice site with some good info on printing with ninjaflex: