Hiya ultra,
Welcome to the start of the process that will bring you the best sequencer in the world!! Firstly, dont take my advice as the best answer, there are a lot of people on this forum, and some are VERY good at building these devices!! Theres always a better answer!!
Dont be too stressed about all of the interconnections as its not as hard as it sounds. The basic rule is to download all of the PDF files from the main site and follow them no matter what. The newer model smash boards look different but follow the same pinning as the PDF files. Any changes are listed on smashes site. His site is also a good thing to have in front of you while building his boards.
With the LCD cable I have made a few and have found that if you put a female DIL connector on the core and on the back of the screen and make a ribbon cable 1:1 between them (dont worry that your connection may not be 1:1) then you cut the ribbon in the middle and label each lead (follow the lead to its source to find the label) and re join them so they all match up again. I suggest when soldering ribbon cable to ribbon cable to tin the ends and make small hooks that then join each other an to put heat shrink seal over the join. This has proved to be the best connection for me so far. This technique is only really for the 40x2 lcds as I have found the pinning never matches the core. If your pinning of the screen matches the core then disregard this.
With ribbon cables you dont need to order them. Just buy some wide ribbon and the right dil connectors and do it in a vice, its much cheaper that way.
Another good tip is to build it all out on a table before putting it into any case. This will make sure it works and give you a good idea of the case size etc needed.
Also, its not the best way to do it, but you can solder the ribbon directly to the pins if you dont want to buy/make the connections. This is actually handy for some connections anyway when a DIL has to go to 2 seperate SIL rows ie core J8 and J9 go to Dout and Din from one DIL set. Of course there are other better ways to do this too.
Another tip is on the smash boards, there may be a DIL there but only connection names on one side. Unelss you have checked that the connection is joined on the PCB with your multimeter only use the labeled pins. An example of this is on the Din boards. I have a DIL connection and was trying to use the 2 end pins as VS thinking they were joined, they arent!
din modules to core (are these configurations correct?):
core (j9) to din1 (j1)
din1 (j2) to din2 (j1)
din2 (j2) to din3 (j1)
Yes that is correct.
dout module to core (and these?):
core (j8) to dout (j1)
Another thing is that if you are soldering to the pins, join the VS earth one first as its always on one end (use multimeter to make sure its the right one back to its source) then work away from the VS cable by cable as they seem to be mostly in the same order. This way you dont need to check which is which as often (only when there is a problem). Maybe I shouldnt share too many lazy type habbits like this tho 
This one is mostly for when connecting boards from mikes shop as there is no label.
the headers on the din modules are 10 pin and j9 on the core is 5. do i only use one row of headers on the din module? if so, which row? how do i know which way to connect the plugs?
J9 core goes to J1 din. Connect each labeled pin to the matching one on the din or dout. 1 row is for the din one for the dout. The DIL header on the core is labeled J8 J9 in the right order. On the din board the 10 pin connections are to go to the buttons and encoders. 8 per set are actually used, one is earth (vs) and one connects to nothing. When using these 10 pin connections you can make yourself a diagram so you can count the ribbon cables (I have the red cable on one end matching the DIL header) and write (after testing with a multimeter) what they connect to for easy reference ie ribbon 1 -> D0 2 -> D1 etc (that might not be the actual connection, check yourself).
if these are correct, in the end will i need 4 sets of 5-pin cables and 1 16 pin cable for lcd?
I think you will need a lot more cables than this to complete the sequencer. Have a look at the pdf files to check, you need connections to the core for each board, also you need connections from each din/dout to buttons, encoders, leds etc.
on the din module, j3-6 are labeled the same. are these connections coming from the encoders and buttons? again, how do i know what to hook up to what?
These all are called shift registers (SR) and each IC chip is one SR. Each SR has 10 pins on the smash version and 8 of those 10 go to buttons or encoders. Buttons take 1 pin, encoders take 2 pins. You can download the PDFs that show the din/dout connections for each application. Here are the ones for the seq:
http://www.ucapps.de/midibox_seq/mbseq_din_v2.pdf
http://www.ucapps.de/midibox_seq/mbseq_dout_v2.pdf
Also with the Aout, if you want to have 8 channels of the CV/Gate buy the Aout not the Aout LC board. You will have to find all the parts yourself, but the only ones that are harder to get are the Maxic 525 chips and the little shunt that goes on the bottom. You can order samples from maxic for these chips if you cant find a dealer who can sell them to you.
If you want a V3 seq you should put in at least 1 IIC board now, and I would also consider an 8 chip bankstick board, and an LTC module to get the most out of it.
With the wiki I dont think there is a manual showing a step by step instruction. I have had almost every imaginable problem finishing mine, so I will try my best to chip in and help you out when I can.
A quick troubleshooting guide when hooking up something and it doesnt work:
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Always plan what you are going to do first, measure things, think about them before doing them and make sure you have all the tools and infomration to do it first. This is especially true for the case, and also for the electronics.
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Always read the PDF first, look at it, think about it, look at it again, then pick up the soldering iron.
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Always check the test voltages before putting IC’s in. This is clearly stated on the main ucapps site for each module what the voltages would be.
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Test for connections being set up correct, use multimeter to beep out end to end. Refer to PDF to figure out what goes to what.
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Check if all IC’s are orientated the right way
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Swap IC’s on the DIN/Dout if all else fails (these IC’s seem to fail a lot I have found??)
I hope this has been of some help for you.
All the best,
John
Good info…
)
:( (Bummer - as I’ve ordered samples from them before.) I’ll be checking back with them later to see if I can purchase them directly from Maxim. Oh well.