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http://www.sudomod.com/forum/viewtopic.php?f=3&t=3148
Hi there - I've been working on a custom board to play along with Kite's SAIO or Helder's AIO boards. I've got a lot of parts ordered for a GBZ build but I'm been weary of using a Pi 3. It's quite large and from what I read it's pretty finicky to desolder and dremel.
I've always had a hard time desoldering big components (I've tried to scavenge from dumpster TVs but it's pretty tough to get the big things off). And the Pi is like a 6 layer board. I didn't want to leave some sort of microscopic bridge I'd never see between the tiny layers and end up frying my Pi 3. I also do NOT want to take a dremel to any of my Pi's because I don't trust myself to not mess them up.
But I still wanted Pi 3 power!

So this is what I've come up with! I'm going to use it with both Kite's SAIO and Helder's AIO boards.
For Kites, I'll attach it with the FPC cable from his Pi 3 adapter board. Then I'll plug in the SD cable and USB cable, and run extra 5v and GND lines to it.
This is the possible placement so far. I'm thinking I'll just need to cut out the cartridge bay and cover it up with part of a game cart on the outside. Once I get more parts in my hands (instead of paper cut outs), then I can see how things go like with the cables plugged in and such.
Here's a mockup if it and Kite's board together. Shows how it might look straight on or flipped down both at once. Since I made this I decreased the size of my board significantly so the images here make it look pretty big. I didn't try to mock up what the cables would look like twisted portrait like I plan to have it in the case.
For Helder's, I'll use the SD Card slot on board and attach the PWM/TV cable to his PWM0, PWM1, and TV lines, as well as USB. I don't need the SD cable on his. I haven't done a mockup of what this build might look like yet.
I just ordered my boards and all the parts, so I'll have more to share soon.
I've been working with @Kite and @Helder in order to make this compatible with their boards, so much thanks to them for all the tips and suggestions.

I'm really excited to finish my build. I haven't seen any hobbyist application for the Compute Module 3 yet, let alone in a Gameboy Zero project! It's been super tough without many other examples of the Compute Module to be able to figure out exactly how to build a board for it. Here's to hoping it actually works when I get it in!!
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Update #1:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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I got some parts in already from Digikey. I ordered them Wednesday afternoon and got them Friday morning! After shipping things from China for so long, I'm used to forgetting what I ordered by the time I get it!
This is the DDR2 SODIMM connector and a 1.8v regulator. I put them on my print out and it looks like they fit at least! The pins are so teeny tiny it's going to be the most challenging/teeny soldering job I've done so far.
This is the size comparison of my prototype against the Pi Zero and the Pi 3. You can see that it's a bit smaller height and width than the Pi 3, but the main advantage is the height gained. My board's height will be about 6mm whereas the pi's is about 18mm. Plus, there's no painful modifications required. And there's no power hungry ethernet/usb jacks either.
The white flap hanging off the top of my paper prototype shows the expected reach of the Compute Module once it's plugged into the CeMu board.
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Update #2:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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More parts from Mouser. The SD socket used in Adafruit builds. I chose this because it will be easy for my to solder the prototype by hand. I also got a book of resistors and capacitors. I chose this one because it had a more curated count per value based on how common they were, plus some of the electrolytic capacitors I've gotten from China before were on spec for certain things but way off assumed specs on others. I wanted to make sure there were no secrets in these parts, so I paid a bit more for them to come from a US distributor. It's still got Chinese characters and such on the book, but whateves. Trust is expensive.
I expect the boards from OSHPark to come in in about 12 days. Can't do anything with the build without those!
I plan to research more about power management ICs and such while I wait.
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Update #3:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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I got the Compute Module 3 Dev board in. This thing is neat, and at $200 it's probably the most expensive electronics tool purchase I've made so far. The next expensive was a $60 hot air station with a soldering iron from Ebay (unless you include Kite's SAIO).
That's all the bits that come with it. You can see it's about as large as the Zero. What you can't tell is that it seems paper thin. I'm afraid that I will snap the thing like a potato chip.
While checking out the fit, I noticed the mechanical key doesn't line up >_< The datasheet for this part was shared amongst like 7 very similar parts and was really convoluted. Also, the Eagle Library provided by the distributor was of a memory module, not a connector. I'll be ordering another 3 of the appropriate ones.
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Update #4:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Just got word that my PCBs have been received by OSHPark and were awaiting depanelization. Then one minute later they had been shipped apparently ^_^
This is a bit earlier than I expected!