It must mean something more than just Jones setting an impossible task, he might as well say a thousand souls. So there's something in the number.
And remember when he said that Will is worth more than one soul, at least three and a half. Or something, then Jones said he's worth one, then 99 souls to go Jack.
Well, that implies that Jack is worth more than Will. Will has been used as a pawn for a lot of things, in CotBP he was used as leverage and in DMC he was used as a soul. In AWE Seo Fang will use him, I'm betting. So will Jones, possibly Jack again.
That's another reason that Jack's the lead male, Will is just a pawn. Elizabeth is the only woman other than the supporting females, she's the lead female. But the supporting character in the movie regardless of gender.
That's why Will was mused as the bishop on the POTC chess set and Jack and Lizzie were King and Queen.
So many hints, if they make AWE E/W they will lose alot of fans and money. And they lost their time in a stupid spanner. These hints are there for a reason.