So far I've been using a clone of a FlashForge Creator Pro, which is the PowerSpec 3D Ultra...which uses the FlashForge Dreamer Firmware, has a touch screen interface, usb and SD compatible... purchased at Micro Center in store for about 699, and been using it for about 4 months now. Now it's 599. I love it so far. Still getting my feet wet, but have printed a lot of useful things so far.

With the included software, PowerPrint which is VERY basic, you can print individual objects, or supports per extruder, and you can set individual travel speeds and temperatures of each extruder for the duration of the whole project. It can utilize Slic3r, Skeinforge and FFSlicer engines for slicing models (.STL or .OBJ) into gcode to be printed.

I'm only familiar with the above, but I literally just bought Simplify3D software, and while I've been reading through all the settings, you can do all of what you are asking about in it. You can configure Multi-Extrusion prints, retract speeds, coast at end, etc....as well as being able to configure extruder settings on a per-layer basis by defining set points in the process settings.

Hell, you can even tell it to calculate how much money is spent on making the print, and how much it will weigh.

Haven't printed with it yet, but as a free software, going to a $129 license software... it's pretty remarkable what you can configure with it.

As for any other software that would allow similar settings and adjustments, There's Cura (didn't have my printer listed), but don't know much about it.