The first one is http://dukesrg.no-ip.org/3ds/rop/?LoadCode.dat&pcout.bin , and the second one is http://dukesrg.no-ip.org/3ds/rop/?LoadCode.dat&pcin.bin . This site should also help you.
I don't know how to resign saves, but you can use the decrypted and possibly modified save with your Gateway or Cyber Saves Editor. If you want to save a save with PKHeX, you have to click the SAV tab, then click Export SAV.
Thank for for helping me test, I'll make a new release with that DLL included. I'd like you to PM me if there are any more DLLs missing, because it'll report missing DLLs one by one, and I don't want to clutter up this thread.