Some one pointed out this thread to me today. I will say this looks great and can't wait to see what the end result looks like. I noticed though you are using the full DS Phat style GBA slot depth which would preclude using DS Lite carts like the DS Lite version expansion card or the DS Lite's dummy slot cover (which there isn't a DS Phat equivalent to...at least not one made by Nintendo anyways). As well as many DS Lite style slot-2 flashcarts.
Perhaps reconsider the idea of having the GBA slot moved off the motherboard so you can better customize it. Perhaps do something fancy like putting it on a slider so you can switch to either configuration on the fly! If slot integrity is a concern the change could be setup to require using screws to enforce either slot position. Just a idea on that though.
It would be cool to have a DS XL where both DS lite style gba carts and DS Phat style carts can live in harmony.
Rebasing the shell design off the DSi XL would be a good idea too. It would make it easier to accomedate using the DSi XL top screen and would making sorting out the ribbion cable for it easier instead of being forced to cheat and use 2 bottom screens.
I wouldn't say you'd directly reuse a DSi XL shell. just rebase the 3D print stuff off it and go from there. It might help with that if you want to try and get the top screen stuff figured out. Plus if you do it well enough you can re-use an existing DSi XL top screen assembly and cut out half the material you have to print. (though on the other hand you'd have to steal the top screen shell off an existing DSi XL I guess)
It might be worth the material cost alone to try that. Just depends on how cheaply you can find used AS IS DSi XL units to use as top screen donars. (oh and using a ribbion cable when setting up the gba slot in this way would probably be best. Using wires is asking for trouble like wire fatigue causing them to pop off their solder points after enough movement.