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I guess i'm wondering if there is anyway to apply shaping to the outbound WAN traffic and not just each interface. More so looking to balance traffic in real time between the vlans and the WAN internet connection without restricting inter vlan communications.
I think the Wizard creates a queue for LAN traffic on the local interfaces that explicitly avoids putting any restrictions on local traffic, so you might confirm that it is working. Is your problem caused by incorrect classification of traffic to the wrong queue? Is the queue bandwidth itself incorrect? Does simply enabling traffic-shaping cause the slow-down? We/you need to figure it out. Look at pftop and other diagnostics to confirm where the problem lies. Share more details.
A possibly simpler method would be to only create WAN queues, but this will mean only your uploads will be shaped. You could maybe use limiters on WAN to shape downloads (queues only work on outgoing traffic) since limiters are capable of shaping in both directions on an interface.