If there is even one input that won't confirm then your entire trx will not confirm.   Unfortunately the bitcoin qt client wasnt written expecting that you would be spending unconfirmed transactions.  Essentially there is no graceful recovery once you have as spend transaction that ends up being a double spend.  

Pywallet lets you remove all transactions and let the wallet fee resync.   That's a hassle for all but us techies.  Maybe transferring private keys to blockchain.info/wallet and emptying the wallet from there might beer the beat path forward for you.