NOTE: this exposes the xprvs for your 2FA wallet, be VERY careful and mindful of the security implications of doing this. An offline computer/VM/Live distro with no networking is recommended.
NOTE: Electrum v2.9+ required (Tested on v2.9.3)
1. Restore you 2FA wallet and DISABLE 2FA when prompted. ("File -> New\Restore -> 2FA wallet -> I already have a seed -> DISABLE")
2. DO NOT use a password
3. On the addresses tab (Wallet -> Show Addresses), right click the address you need to sign with and select details, this will give you your redeem script.
4. Goto https://coinb.in/#verify and paste your redeem script (Note down the 3 public addresses it gives you)
5. Find your "restored2FA" wallet file (%appdata%\Electrum\wallets) and open it in the Text editor of your choice. You should find sections labelled "x1/" and "x2/" that contain your two xprv "rootKeys":
6. Create a new wallet using the "x1" xprv ("File -> New\Restore -> Standard wallet -> Use public or private keys -> Paste in the xprv")
7. Look in the addresses tab for a matching address from step 4, right click and "sign/verify message"
8. Sign the message required
9. Repeat Steps 6 thru 8 with the "x2" xprv.
10. Make sure you have deleted the unencrypted "restored2FA" wallet. or alternatively, move all your coins out of your 2FA wallet as you should probably consider it compromised.