As it happens I am back in kraken now, and my funds are still there.
If i understood you correctly, you are back in control of your Kraken account and your funds was untouched. That is a mystery, if you were truly hacked, the attacker would surely have moved all the money you have in your account.
I set up 2FA, now I can't log in, I am checking the google authenticator app but no codes are appearing. This is truly a balls operation.
Did you set everything correctly, because if you did, you should not have any problems such as this one.