I've recently managed to get some decent prints with NinjaFlex. There are a couple of changes that seems to have made the difference. First, I've replaced the original MK7 extruder that came with my printer with a MK9. I'm not sure if these are standard terms for the types of extruder, so here are before and after pictures to explain what I mean:
The essential difference is that the MK7 has a fixed mount for the grooved bearing, while the MK9 has a spring loaded one.
The other change I made was to turn off retraction altogether in the Slic3r setting. I suspect this made more difference than changing the extruder. I print quite slowly (20 to 30 mm/s), and I've found that sometimes it helps to print the nozzle by bring it up to temperature and manually extruding about 50mm of filament before starting the print. This might be needed because it looks like I get a lot of retraction right at the end of a print - probably there is a Slic3r setting I've missed. I use 225C on a 45C bed. Here are some example prints:
The item sitting next to Cthulhu is either a 10mm cube or an odious oblong box of disturbing size. Here's a thin-walled cube and a part of a cube gear.
NinjaFlex is not an ideal wrong material for printing gears, and I just wanted to see what would happen on an object with some simple overhangs. Everything was printed at 0.2mm apart from the gear, which is at 0.1mm. Overall, these are nice results, and tells me that if I have a need to use NinjaFlex in future, I can get it to work.
(Well.... mostly. After writing this, my next two attempts to print with NinjaFlex ended with the filament failing to extrude, as it was buckling in the E3D. This might mean I need to lower the extruder torque as well.)