I made something similar and this works good: Just take the standard PCBs from ucapps.de or smashtv´s PCBs and copy/paste it together as you need it onto you format (e.g. 160x100 with core+LTC+some DINs or so). The interconnections are then just soldered permanently.
MUCH less effort than making everything new in Eagle and a piece of cake, too.
The ready PCBs (for copy&paste) can also be found as .pdf´s in the portal of midibox.org.
i have quite a few custom boards I have done and each one seems to be specific to my application for that box.
I have also found that cutting and pasteing is the best bet with a few hard wires.
it won’t be rocket science. My Moog Modular V is 2 X (6in. X 9in.) boards with
1 core
2 ains
2 dins
sorry no douts… but again… there’s that connector for that and it’s not rocket science
happy to give you the pdf’s of these files… sorry I take eagle files, turn them into postscript files then edit them in photoshop to get wider runs and bigger pads… etc, etc, and of course, etc…
the final pdf’s are printed 1:1 and work perfectly.