Bryan has been running a customized version of the firmware from pretty early on, he adjusted down the speed and acceleration for the motors to what he found they were capable of in the real world. A month or so ago Colin at MakerFarm made some very similar changes to the firmware he ships, so you are probably good. If I recall correctly the first thing Bryan did was rig a rPi to his printer.... I never did this because I had a spare PC to connect to the printer which I can do my 3D design work on and have it control the printer, I kinda like to watch the layers go down on the Pronterface 3D view anyways... Bryan also added an optical end stop to the Z-axis cause the screw/switch system is a little hokey. I never did this either, however, I did find some screws that bite the holes in the micro switch well and used them to secure the Z-Axis switch to the frame, and I also put some solder wick into the hole where the adjuster screw goes so it will bite better. So far so good with that, I really haven't had any problem with it...
I had some problems with my bed hitting the Y-idler (on the single bearing side) from the get-go. So be careful how much to tighten down the bearing on that side, if you crank it down and the bearing bites down on the wood enough to round the edges of the slot the bed will sit low on that side. I had made Colin aware of this issue so perhaps he has made changes, however, the bed was extremely close to the Y-idler on both my kit and Bryan's. I printed up a pillow block that I use on the bearing(s) to secure them in place (rather than having them pressed right against the wooden bed) to raise the bed a little bit, eventually I made a whole new bed out of an aluminum plate (very happy with that, it sits much more level than the wooden one, which always wanted to dip down on the single bearing side). I also secured the frame of the printer to a wooden base, cause the Z-towers had a tendency to wiggle, if I barely touched a Z-tower I could see it (the whole frame) move quite a lot, the movement of the hotend over the glass when I did this was very pronounced. Once the printer frame was secured to the wooden base everything was MUCH more stable....
IDK if Colin made any changes in this area, but the way the steppers are wired you kinda need to plug them in upside down, RED wires on the TOP. I think the diagram provided with the kit is generic and actually showing the wires in the wrong order. (not sure if he has changed that or not, but RED wires need to be on TOP) Good news is if you plug them in upside down (as shown in the diagram I got) nothing will burn up, but it is kinda shocking when the bed and extruder race in the wrong direction when you hit home, if you don't yank the power they will hit the end and the belt will start to skip. (very alarming!) You can invert the direction for each axis in the firmware if you like, which I did at first, but then I realized I would have to do this every time I updated the firmware which is a PITA, so I ended up pulling the wires from the molex plug and installing them in the opposite orientation (RED at the TOP).
That's all the stuff that comes off the top of my head about my initial experience with the MakerFarm i3 kit.... Good luck with your build.....