Thanks @Patrick Brunschwig for the quick response. You're absolutely right, I just changed the setting over to prefer OpenPGP over S/MIME and everything just started to function as it should. Clearly I was thinking in the wrong direction regarding the public-private key linkage. But then again, looking at the error, I cannot really blame myself. Is is a bit hard to link it to the actual issue. Thanks again.
I'm experiencing the exact same issue (EnigMail 2.1.7 on windows),... keys-pairs were generated on other machine, private keys exported to OpenPGP applet on Yubikey, public keys exported and imported to GnuPG on email machine. Yubikey 'Card' visible on email machine, through 'manage card' menu, however signing an email always runs into the issue: "You specified that this message should be digitally signed, but the application either failed to find the signing certificate specified in your Mail &...