Hello again,
After a couple weeks of experimenting with the printer and software I have several more questions/requests for advice and comments to share (most of the comments will probably be things that are obvious to most of you but perhaps other newbies out there would benefit, or you can correct me on some of them)

I've been mainly printing with the MakerGear PLA so far. I've been using either Slic3r or Simpify3D to generate the G-code, then the free Pronterface/printrun thing to start the print (I like the simpler interface).
Comparing Slic3r and Simplify3D - The default settings in Simplify3D didn't seem to work very well for me, even though I loaded the MakerGear M2 V3b hotend profile. Specifically, the print wasn't sticking to the bed very well. I ended up trying Slic3r as well to compare and had almost the opposite problem...the bottom layer was almost liquid which caused the whole part to end up kind of warped and uneven. Looking through the settings I figured out that the difference was mainly in first layer height...Simplify3D had it set at 100% or greater (don't remember exact value) whereas Slic3r was literally burying the first layer in the print surface (z was negative). So after playing with different settings, 5% seems to work pretty well for me. It also seems like the slower the first layer gets put down, the better. I've been using values less than 50% for the first layer speed.
It seems that when you print through the SD card with either software, actually hitting "disconnect" once the print has started will turn the printer off. However, simply exiting the program or unplugging the USB allows the printer to continue printing. Interesting.
A code question - what is the difference between M108 and M106? A lot of the documentation on the M2 I've looked at uses M108 to turn the fan on. But turning the fan on with M108 doesn't seem to work for me. Also even when I use M106 the fan seems to be either on or off. For example if I send "M106 S255" to the printer it turns the fan on, but "M106 S100" doesn't do anything. My understanding (which could easily be wrong) was that S100 should set the speed to basically 100/255 of the full speed - 40% or whatever that is.
I've been using fine grit sandpaper to wipe my hotend clean of the filament that inevitably collects on it. It seems to work great. I'm using very light strokes but am I still in danger of eventually wearing down the nozzle? What do others use to wipe the extruder?
Now I'm trying to print ABS on Kapton tape with the hotend at 240C and the bed at 110C. Instead of re-calibrating the machine, we just measured the thickness of the Kapton tape and added that to the 5% first layer thickness, which gave us 32%. It seems to work okay most of the time but certain parts will not stick to the bed well with those settings. Should I decrease the layer thickness, turn the nozzle temp up more, or both?
Got a couple other questions already concerning ABS...
- How often do people re-apply the Kapton tape? Not after every print, right? Just whenever it's needed?
- Simplify3D isn't turning the fan on at all when working with ABS. Did you guys configure it to turn the fan on or is it better to leave it off? While I'm at it, what fan settings work best for PLA? Simplify3D was turning it on after the bottom layer and Slic3r didn't turn it on at all. This might be related to my "code question" above too...
Sorry, I know this is a lot all at once. :p thanks in advance!