Nope, sorry. If you can't afford to make the whole batch, you can't sneak around the cost by making fewer arrows. (You can't make a wand with fewer than 50 charges, either.)
I actually think you can get around the cost that way. Maybe its in Tome and blood but I'm fairly certain they mention making items at less than 50 charges somewhere.
I think you can. I'd certainly allow it. You can make wands and staffs with less than 50 charges, after all. And the peerless archer has an ability to create magical arrows without the prerequisite caster level or feats (AFAIK) and there the arrows are priced separately, too.