It sounds like you're saying that everything seems to work fine until you actually try to link an app through link2sd.
I link using the link2sd app. In fact, it's set to automatically link anything installed, so it just does it and puts a notification up that it did so, and nothing outside (except for the initial setup) is needed to do the linking.
Do you get any sdcard errors when you boot up?
All I can think of is if you have another (even if smaller) microsd card to try out from a phone, mp3 player or other device, it might be worth seeing if you can at least make that work. On the PEs I'm using 8gb cards, but on my phone, I'm using a 16GB card without any problems. I had to use an ext2 partition on my phone, but don't know if that was just a limitation of my phone.
I'm not sure about the storage issue with the app you're trying to install, but it might be related somehow. Can you store other files manually on the sdcard (like downloaded files or transferred files) without issues, and are able to open them up to make sure they work okay?
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