I need to find another slicer for now due to a Slic3r gap fill problem in Slic3r 1.2.9 that affects the printing of thin airfoils. It’s halted my ability to develop. Is there another slicer I should be looking at for multi-extruder printing? I’m about to give Cura a proper go.
Have you looked at craftware
What is the specific problem? Just curious.
In slic3r? It over extrudes during gap fill. This has a bad effect on quality of thin prints. https://github.com/alexrj/Slic3r/issues/2960
I got Cura all setup! The only problem is I can’t specify which extruder to use for which part. Frustrating. 
I have not tried Craftware, investigating.
[edit: I investigated, it doesn’t appear to support multiple extruders]
I know from a guy who is experimenting with multi material printing (3 color) and recently stated that Cura works fine for 2 material.
I also heard nice things about kisslicer for multi material prints, you should try it.
Tx for the Kissslicer and Simplify3D ideas, these will be next up. I’m doing a test print with Slic3r 1.2.7 right now as I understand this problem may not be present in that version.
Have you tried slic3r 1.2.9? 1.2.7 is a beta version, maybe they have fixed that very same issues before launching a stable version.
So 1.2.7 produces some better prints but not perfect. To print multi-material with Kissslicer I must cough up 45$, Simplify3D is 150$. I think I can make Cura work. I wish it allowed me more control over which extruder is assigned to which part.
Try Mattercontrol with Matterslice, its great 
I love kissslicer it has the best support I’ve seen and I love that you can specify a wall thickness that not just loops, it means you can make the strongest lightest parts with it
As for printing multiple parts I used to use repetier to lay the parts out any then save that as an stl file to use in kissslicer
Can recommend CraftWare. It is not very well known yet but for me it works greatly.