I had problems with the controller. I managed to get it to be wired up ok for the memory pack (they arrived this morning), great I thought, hot glued the controller part, great, still works; carefully hot glued the other part, initially ok, finished hot gluing and then I got an error from the memory pack. Of course, hot glue in place, you can't see what the issue is and resolve it. In removing the hot glue I yanked off a couple of contacts from the controller board, so gave up with it out of frustration!
I then got to think - originally I planned to have the joystick on top of the N64 mobo, so I had to relocate the memory card slot for this purpose, as otherwise the overall height of the console would be too high. As the controller will be UNDER the N64 mobo now, there is extra to play with. The height of an N64 cart is 18mm, the height of the N64 underside metal sheet is 4mm, case for the N64 cart will be about an extra 4mm, the height of the N64 mobo up to the fan is 38mm. This gives me a maximum of 64mm to play with. The controller board, memory slot and memory card is 50mm. This means there is no benefit anymore of relocating the memory card (and much better airflow to without all those wires). Quite pleased about this, because although I got the previous controller to work fine, the joystick isn't as good as this one; also the joystick has a flat top so I don't have to hack away at it as I did with the last one (I want the top flat); and the buttons are all the same height, which is better.
If this guide gets onto the Wiki (hope it does), I will remove my previous postings about the old controller and relocating the wires for it, as it isn't relevant to my mod anymore.
Anyway, here is a pic of the controller:
And opened, notice the joystick, it is quite large, operating height is about 32mm; a bit higher than the other one, but is better, so will use this one now. Had to get rid of some of the hot glue the manufacturer's put in the case so I could get the mobo out.
Here is the other side of the board, nice and easy to connect button contacts onto!
Because of the butchered controllers I have hacked to this date, I have several button contacts like the one below. This means I have the choice of either using tact switches, or the rubber contacts, which I can locate anywhere I want to on my case. I will probably still use tact switches though as easier to work with (I will experiment).
Below is a rough WIP plan for the case's insides (ignoring wires and controls). Only rough! Plenty of airflow (not shown very well on pic, but will basically start via airholes by the cart slot, air will run over all three mobos, over N64 board and out above the heatsinks.
It would have been nice to have had the console flatter, may still be able to. Can't find a dead quiet fan under 25mm deep, 15mm would be ideal but they are not quiet enough. This adds to total height unfortunately. Visiting shops tomorrow to see if I get lucky and find one. Lots of planning and experimentation to do yet.

Pity the joystick is so tall. I might see if I can get a third party suitable joystick (eg GameCube) use that instead, and decrease the sides from about 34-36mm high to more like 20mm deep, however, c. 34mm quite a comfortable height for adult hands...
I anticipate the width of the case will be about 25cm and the width about 14cm; keeps it quite small, in the circumstances.