Thanks. Yes I've read a warning about using non-12 character seeds, but this was unfortunately the only path I could use at that time.
Is there a way to modify this seed (like how v2 uses an extra word) so that it will contain the version/checksum and can still be directly entered into v2?
First of all can you please confirm that my method above worked? I'd like to know in case others face this problem in future.
To answer your question if you modify the seed you modify all the private keys and all the address. So it isn't possible because it results in an entirely new wallet.
You can create a new wallet if that's what you want. Try this command in your shell/OS command line:
electrum --nbits=256 make_seed
The above command will make a 25 word seed with 256 bits of entropy. You can then do a wallet restore specifying this new seed to create a wallet with it.
electrum -w /path/to/new_wallet restore
You can then send your bitcoins from your old wallet to this new wallet.