Okay, what the hell?
I tried re-downloading the same a9 file from Gateway-3ds's site. same hash, same link. renamed and verified things before putting it in the 3DS again. And now it works?! Was literally just dealing with Steam this morning deciding it didn't want to launch anymore to the point I even tried reinstalling the whole program and it also not wanting to work, and then just not even an hour later, it started working again.
Okay, so GW is working again... one exasperated me later.
Still not sure how to get around the GBA/DSiWare problem, yet.
Even so, was also trying to see if/how freeshop is better than CIAngel. My immediate problem with CIAngel is that it flat out doesn't list even half of what's available in the real eshop. But if I run freeshop, it just tells me it needs some enctitlekeys file, but I couldn't find where or how to make it.
... I think I should head to bed, before I break something irreparably.