Storage
Space on your SD card is not unlimited . I suggest you delete a downloaded content that you don't need ,maybe ? If not you can always grab a few SD card for 3DS/XL.
You can buy SD cards on sites like The Official Nintendo Store as well as eBay,Amazon and Argos.
SD cards in the Official Nintendo Store here
All compatiable SD cards are :
4GB SDSDRX3-4096
8GB SDSDRX3-8192-A21
16GB SDSDRX3-016G-A21
32GB SDSDRX3-032G-A21
8GB SDSDXS-008G-A46
16GB SDSDXS-016G-A46
32GB SDSDXS-032G-A46
16GB SDSDXP-016G-A46
32GB SDSDXP-032G-A46
8GB: RP-SDUB08GAK
16GB: RP-SDUB16GAK
32GB: RP-SDUB32GAK
8GB LSD8GBBSBNA200
16GB LSD16GBSBNA200
32GB LSD32GBSBNA200
Payment
Yes you are probably wincing at this word, but you have to pay for Pokemon Bank.
This fee is ¥500 in Japan, $4.99 in the United States and Canada,
£4.49 in the United Kingdom, €4.99 in Europe, $6.50 in Australia,
$8.50 in New Zealand, ₩5000 in South Korea, $150 in Taiwan, $40 in
Hong Kong and R$ 8.99 in Brazil.
Contact Nintendo
If nothing works the only thing you can do is probably contact Nintendo.
Or you can go on their Tech Help Forums