I'd use Coin Control to select the inputs you want, and send the entire amount with the lowest possible fee. Then make sure your wallet keeps broadcasting the transaction. See
my topic on consolidating small inputs.
Just in case, I'd keep the transaction under 10 kB. It might be easier to fit a block that way.
Thanks, will check it out. So, what you suggest is that if I have 40 small inputs that I would like to consolidate, it is better to make 4 transaction each with 10 inputs and 1 output?