So here's what I've found:
The duplicated profile does not give the correct g-code for the left extruder. I don't know why (bug).
I exported the same object using the default standard, and the duplicated profile (as gcode instead of x3g) and compared them in a text editor. The tool change and temperature settings were for T0 instead of T1 - there's the problem. Somehow the duplicated profile doesn't respect the extruder choice per object.
I manually edited the gcode, then processed it with ReplicatorG. Then tried printing - but my gantry wouldn't home properly (kept crashing) - I didn't investigate why - I didn't change any homing gcodes.
So I reverted to simply modifying the standard profile to match my desired settings. (I'm trying TPE).
And, after a few clogs and messing around with the soft filament, I was able to half print a small test house object. Pretty good (it came off my bed - I will try helper discs or raft next time). The stuff is flexible, yet really strong - even with 2 walls and 10% infill. I could not destroy it (only 5/8" square though, so hard to get a good grip).
Anyway.... That's where I'm at.