I spent ages (a good hour or so) turning the GBA around, putting the two GBA boards together, placing them on the N64 (making sure I used electrical tape to stop shorts) and trying not to tangle the many, many wires. I didn't want to do something silly at this stage and either snag a wire or make a short. I then secured the GBA mobos in place with a couple of wires (non conductive), hot glued across the distance of the GBA mobo; then a good sized blob of hot glue securing the rear of the GBA cart slot to the N64 mobo. For extra strength, when I am able to turn the whole assembly over onto its front (when mounting the buttons in the case for example) I will secure the GBA cart slot to the N64 mobo underneath too.
I needed access to the GBA cart under the case, and as little of the GBA mobos across the space where the buttons will go as possible. Unfortunately, to get access to the GBA cart I had to go over the button area a little more than I originally intended, so I might need to relocate the Start, Select, So-mo and GBA menu buttons to the other side of the case, to the right of the D-pad; I won't know conclusively until I can see with the top on how much space I have to play with. I have to keep the GBA mobos high, as the idea of the case is that the fat bit is all the electronics for the systems, and the thin bit is the rest of the case (where you hold the system).
Below is a pic of the system as it is now, with the fan in place for illustration purposes.


"A" is the GBA board, "B" is the GBA mobo underneath it and "C" is the fan.

"A" is the GBA cart, just visible.
You will need to take my word for it as I couldn't get a good camera angle, but the height of the highest part of the GBA boards (the capacitors) reach 55m (approx) from the table, and the top of the fan is also 55mm from the table (approx). This means the final height of the thick part of the system will be around 70mm tall.
The other thing which will be a compromise potentially is that I can only get the GBA cart access in one place, so I will have a "bulge" under the case for the access. I was hoping not to have this issue, so I could have put the GBA mobos elsewhere, but as covered earlier, my attempt at cart relocation for the GBA ended in tears before.
UPDATE:
Ok, thought around the problem; I will re-do this tomorrow - if I reverse the GBA section upside down and over onto the area where the pins are for the N64 cart, the GBA cart will be facing upwards. If I then reverse the case entirely so the fan is at the underside of the case, the GBA cart will be at the base of the system, and accessible; where it should be. I also shouldn't have the issues with the actual case itself being an odd shape.
Oh well, most of a morning's work lost! I hadn't appreciated all the issues until I had done the work... anyway, it is worth doing this job right!
This will mean extending the buttons to the joystick and buttons as they will all be on the opposite sides now. I will have to drape the wires over the N64 mobo area; it won't affect airflow, and you won't see anything when the case is on, so it doesn't really matter how this looks.
More updates tomorrow...















