Well wood is pretty easy to come by and work with to build that box, The entire thing can be done under a couple hundred if your smart about it. I suggest that you just take your time and shop around for the small parts see what you can find. Theres no rush, just take your time and shop around.

The veging box should be smaller than the flowering box but 2ft is a bit too small I think. Unless you've got your crop rotation schedule down to a T your going to regret the size if some of your mothers are late in veging or flowering and your veging plants start to outgrow the box.

The rest of your questions Ill leave to the more experienced growers to answer.