We did Group's program last year so I know what you're talking about. I think this is one case where getting everyone signed up in general with a mandatory question of Grade/Age may make the most sense. After that, probably have a party to move people around. I don't know how your VBS runs, but we always get requests of "please put Jane in with Joan because they're best friends" and the like. I can't even imagine trying to manage that with assignments coming straight in from a form.
I'm hoping one of the delivery people has a better idea on how to handle VBS registrations for mixed age groups, but I know we ended up using a whiteboard of some sort and sticky notes to form the groups (of course my church is much smaller than yours :) ). We had people reviewing the groups as they were forming and moving people around and kept the registration to each group equal while splitting up/pairing certain kids and/or leaders.
Does Group have a Preschool program this year like they did last year? If so, you'd want to include that as an option when filling out the forms. Perhaps create one RLC for Preschool and another for the "big kids". Assign each to breakout groups to handle them splitting up and/or coming together. I guess you could even consider multiple RLCs if the large groups are getting too large.
In Him,
-Peter