Did you have any issues with the secondary extruder? I have the same printer as you but the second extruder step setting is way off and looking for some insight.
I'm not quite certain what you mean by the second extruder step setting. Unless I missed something, there's only one step setting for both extruders.
I bought two new stepper motors for the extruders (so they would match), and then had to change the rate to get 100 mm of filament for a command of 100 mm. They did not not feed the same as the one that came with the printer, and I'm not using that motor right now.
With the older version of Cura (I haven't used Slic3r, so I'm not sure about it), there is a setting for the offset of the extruder nozzles, but the same setting is available in the Marlin firmware. Don't set both of them, only one. Otherwise, you end up doubling the offset. Made that mistake first, and ended up with the two dual extrusion test crosses offset when they print.
A number of changes to the firmware for the dual extrusion and the PID settings for the hot ends. I'm still working on some fine tuning, but I've manged to get some acceptable prints out of it.
If you can be a little more specific, I might be able to help more.