You need to pay 0.1 mBTC per 1000 Byte of your transaction.
1 input is about 180 byte.
So if you have 1000 Inputs you'll need to pay at least 18 mBTC or 0.018 BTC to send it.
There is no going around that.
And how much time it would take to confirm?
As long as you pay the min fee, it should get included in a block soon even for a huge tx.
It might take a bit more time if you pay min fee, but it will eventually get confirmed, because some pools don't take low-fee transactions.