Once you fly the stack you will appreciate the padded handles, yes, you will want those. The loops are ok, so is tying the tails -- you can sew in a new loop, or just tie on -- your choice. Yes, you will need the lower frame member, graphite or not, graphite is stronger (and lighter). The sail on the leading kite is likely to stretch more than the others, so a bit longer to tighten the sail would be good. As far as storage goes, whatever you want to put them in will work for you. The rubbermaid container is fine, as long as it stays dry inside. You can use some dessicant to absorb any moisture, so the sails don't get mildewed.
I hope this helps a little bit. I'm sure others will help you with your questions more than I can.