Hi there Simon! Welcome aboard!
If the Makita has a fixed base that you can attach to the sled, you should be OK.
Really, any of the boards Ryan offers will serve you well, but the Rambo and mini-Rambo probably have the most hours (and therefore experience) behind them. But there’s lots of exciting things going on with the SKR and Archim boards (if you’re in to exciting things happening with your controller).
As for 3D milling, that’s a bit of a loaded question. Build as designed, none of the V1 router-based machines do “real” 3D milling. They can do a really good bas-relief style of 3D milling, and are excellent at 2D milling. 3D milling on the Lowrider is a little tricky, depending on the size of your build. If you’ve got a 4’ Y axis, even with the two rails, it’s going to have some flex. It can still be done quite well, but you have to know your machine, and know your CAM.
As for software flow… Hoo-boy. Read the milling basics page for the bog standard workflow. You can generate your artwork in anything you are comfortable in, as long as you can export it as either DXF (for 2D or 2.5D), or STL (for 3D). Once you have your artwork, you get to do your CAM work, where you actually turn that art into the gcode that the machine understands. The default workflow is to use ESTLCam, but there are too many different programs to list that can do CAM (a lot of design software now includes CAM, such as Fusion 360 and OnShape [via Kiri:Moto]). Note that this can get troublesome since there are different “dialects” of gcode, and you need to make sure your CAM software is creating the correct version for your machine. Once you have the gcode, you have to get it to the machine. If you have an LCD (or a new-fangled TFT), you may have an SD card reader you can simply move the gcode with. Otherwise, you’ll need to use a gcode sender/machine controller like Repetier Host, pronterface, CNC.js, or even Octoprint (the last two are also on the v1pi image created by Jeffe for running your own Raspberry Pi print server).
That’s a lot of information I just dumped on you. Take your time to read it, and ask questions. We really don’t bite. In the meantime, I have a question for you: What are you wanting to do with your CNC? It would help us understand your needs better, and give you more appropriate advice.
I strongly urge you to poke around the forums, read a lot, like helpful or entertaining posts, and generally join the collective. If you have any questions about actually using the forums, just ask @discobot, who is here to help.