Hello, welcome to this project.
At this point I've received all of the major components for this upgrade (motherboard, extra stepper, extruder frame blocks, hot end), and printed out all the needed mounting pieces.
The only part I had to design from scratch was this mount for a second extruder stepper. I designed it to mount between the z-axis carriage and the first extruder stepper, with the mounting holes for the second stepper extending out to the side.
Based on the CAD model I thought I designed it with enough clearance for the lead-screw threaded piece, but that ended up being more obtrusive in reality, so I had to hack a big chunk of the mount off in that area:
After that though it fits pretty nicely on the z-carriage:
only other thing to note with that mounting scheme is that the screw holding the inner z-axis bearing protrudes out just enough to conflict with the first stepper after it's lowered an 1/8" relative to the rest of the carriage because of the thickness of the new mounting bracket. There was a washer on that side of the carriage though, which when moved to the other side reduced the amount that screw protrudes just enough for the stepper to fit.
I'm still waiting for some longer socket head screws to be able to mount the extruder frame block to the stepper through both the z-carriage and the second stepper mount.
The hotend mount from krestoverson (https://www.thingiverse.com/thing:2854282) fit very snugly around the mounting holes on the x-carriage, so I don't think screws are needed for that:
The original heatsink cooling fan needed the printed adapter (https://www.thingiverse.com/thing:1049548) to fit, but as krestoverson noted you can't use the 12V fan that comes with the hotend since the ender 3 supplies 24V power. The mounting slot for the part cooling fan didn't print properly, but I should be able to still hold the fan with a washer for extra support area.
Assembling the heater blocks was kind of tough to figure out since I haven't done anything like it before but I think I'm on the right track. I'll definitely add washers to the screws that are holding in the thermistors (didn't come with the hot end kit). I also had to separately purchase the 24V heater cartridges, as the kit comes with 12V cartridges. The thermistors come already sealed in tubing and with heatshrink at the joint between them and the wires going to the control board, but the wires are bare ended so I'm waiting on the proper crimp connectors to interface the thermocouple with the control board. There were various online resources I followed to figure out how to put this part together, the most helpful was from the E3D wiki (https://wiki.e3d-online.com/Cyclops_%26_Chimera_Assembly), but I haven't heated it up yet because I'm waiting for the thermistor connectors so I'll wait to call that a success until I've actually heated/tightened the nozzles and get them level. Also waiting on the thermal grease which is recommended for getting good heat conduction from the throat to the heatsink.
Finally the motherboard enclosure from TeachingTech for the MKS Gen L was simple enough to modify for the Base board.
It has the same Rs values for the stepper drivers and the same family of drivers (A498...) as the Creality3D V1.1.4 board that came with the printer, so I read off the stepper Vref voltages on the stock board and adjusted the ones on the MKS Base to match as close a possible. Knoopx had measured Vref values on his stock V1.1.2 board (https://gist.github.com/knoopx/e6c40a009e796203b93a75a3ed6a5ab8) and the values I measured were more-or-less the same:
For the stepper I ordered for the second extruder, which has a 2A current rating, setting the driver to 90% meant trimming the Vref to 1.44V.
I've attached the current marlin firmware configuration I'm using (rev1 9/25/20).
I had to compile it with platformIO, there was a weird bug with using the arduino IDE because of how long command line instructions can be.
Also of note, the EXP1 and EXP2 connectors on the MKS Base are upside down, so I had to chop off the orienting nub on the ribbon wire connector and plug it to the board upside down to get the display to work.
Will update once I have the additional screws and crimp connectors and hopefully will have the new hotend up and running and ready for tuning.