I've done it (DIY MK7)but why MK6 motor (other than you have one)? The MK6 can run 1.75mm filament with the single piece PTFE tube that solved 90% of the problems and then the new 0.40 nozzle is basically the same for either a true MK7/8.
PTFE tube for 1.75 http://store.makerbot.com/machined-core-tube-for-mk6-1-75-mm.html
Nozzle
In other words, is it because you have an early MK5/6 with resistors, before they came out with the MK6+ cartridge heater, and thus you want cartridge heat and 1.75mm filament? If you have the old resistor setup, then you need the stuff on this page
http://store.makerbot.com/catalogsearch/result/?q=mk6
Heater block $30
Core heater $28
Safety thermostat $8
Safety cutoff $22 Do not use a core heater system without this!
You would basically need the same parts for a MK7, minus the heater block as you have to make a different one.
Further, let's talk about the motor. You need the big motor to push 3mm filament, but do not need that big motor for 1.75 mm. Further, that motor was custom with a 6mm shaft, to match the original MK3-5 series DC geared motors because MakerBot had a ton of the 6mm bore pinchwheels made. They now have a ordered a ton of the 5mm bore version which matches 90% of the long body NEMA17s avaialable. Thus, last night, I tried a http://ultimachine.com/content/kysan-1124090-nema-17-stepper-motor for $21 (with connector) driven by a gen4 stepper driver and MK7 pinch wheel and it extruded 3mm filament fine via a MK6+ basically stock. The reason I mention this is that the stock filament pusher system with the Delrin parts has a great deal of friction. Many of the printable bearing pinchwheel parts on thingiverse can greatly reduce the friction the motor sees and give more push.
http://www.thingiverse.com/thing:32108 (Note: only works with 3mm filament but very good)
http://www.thingiverse.com/thing:16562 Custom 1.75mm filament drive-unknown if it can work with 3mm?
http://www.thingiverse.com/thing:14468 Another 1.75
Ok, so let's say you are dead set on making a MK7 clone.
I'm assuming you don't have a CNC mill or else you likely would have asked.
The easiest way is to print off some parts to use as templates to cut and drill the metal parts.
First, print the filment guide block
http://www.thingiverse.com/thing:16179
Bolt that directly to the motor with no cork gasket and remove the pinch wheel for now. The part we care about is the filament path because that helps us locate the exact spot on the aluminum block below we drill the hole for the M6 threaded tube to fit into.
Next, I would print the metal blocks for reference. Here is a great picture of the final part you are trying to make:
They make great drill guides and this is the easy way I made mine in a drill press. I had a milling vise (a vise on the drill that can move in X or Y to position the hole exactly lined up, rather than reclamping the part each time). You also need a set of metric taps, or just the M6 and M3 ones with matching drill bits. I also have a massive set of numbered and letter drills to step up the hole in very fine increments. For an M3 thread in aluminum, this is the only way to get it "right". The parts to print are best found in the Replicator on Thingiverse
http://www.thingiverse.com/thing:18813
You want the STL zip
http://www.thingiverse.com/download:60679
In that massive xip, you want only 2 parts
The dual extruder baseplate
The aluminum heater core blockThose 2 parts are critical, and the key part is that M6 threaded hole placement. Also of extreme importance is how tight the threads are on that hole. Both need the best thermal conduction to the threaded tube and nozzle as possible. The heater block must interface the nozzle and transfer the heat. The tube must then also have any heat drawn out of it at the top by the aluminum block on the motor, The placement of the hole in the motor block must be exactly in line with the filament path. Finally, the 1/4 in hole for the heater must be a tight fit. The other kicker is that in aluminum which expands a lot when heated, those tiny M3 hole can get loose, thus, the drilling and tapping operation on them must be perfect, if not a little undersized. The same is true for the M6. If you don't have experience, making those 2 parts can make or break the whole thing.
Finally, the missing piece you need is either the original tube from Makerbot (must contact support and they want $10), or get a similiar tube from Makergear
http://www.makergear.com/products/plastruder-replacement-parts Note that you can get 3mm bore or 1.75mm bore. I was able to get one of the experimental stainless ones a while back seen in this picture here of my custom, copper hot end
Alternatively, you could just get the makergear nozzle which screws over top of the M6 tube, but I say that's not as good because of the extra thermal interface. I say that because thermal interface 1 is heater core to the block. Interface 2 is the block to the tube, and interface 3 is tube to nozzle. Remeber the thermistor or thermocouple is sensing the block, not the nozzle, thus they can and will be at different temeperature if you are picky.
The key here is that I tried to optimize the design by using a copper block, super tight finish on the MK6 threads to ensure maximum heat trander to the nozzle. At the motor end, I also made sure the fit was perfect and used a thick aluminum mount to further sink the heat away. The turned down section of the stainless tube further reduces the already low amount of conduction upwards towards the motor. MBI uses the exact same thing on their tube (sorry I don't have picture).
All that said, the MK6+ is a good system and supports both size of filaments. I would stick with that, over a ton of machine work that may or may not be as good as the MK6. One area of improvement for both is a bearing filament drive. There are tons of them on Thingiverse (just search for MK6, MK7, or MK8). Some could work with both sizes.
Again, let's recap the "why" behind this. MBI made it's decisions on cost, not what is the best part. MK6+ is a solid design if not for the filament drive. MK7 was about cost reduction as the lower parts count and lack of laser cut parts was key factors in the design. There are some improvements because of of the ultra short filament path and no PTFE in the nozzle, but not enough to justify the pain you are going to go through to make your own.
There are some avantages on a MK7/8, but only seen in special circumstances. One factor is the moving head design in Replicator as the mass of the motor must be moved and can lead to skipped steps. I know for fact on another bot project (Type A machines series one, also on my flicker pages) is a moving head and weight is a factor. Thus, I measured the weight of several motors.
MK6 motor is ~500g!!
Ultimachine motor ~440g
Moons motor ~ 220g
The Moons motor is what they use for the MK7/8 and also every other motor in the T-O-M and Replicator series. Thus, if you have a moving head, and you want to print with 1.75mm filament, than the larger MK6 motor is not the best choice. If you have Cupcake, T-O-M, or other printer where the head only moves in the Z axis, then the bigger motor is not a mass penalty. This is the second part of "why" I asked your intentions behind the custom build using the MK6 motor.
For the most part, upgrade what you have with the PTFE tube for $15 and be happy, maybe a printed bearing filament drive would be good too.
