Routing through the thickness of any plywood can be a real nightmare!
I also have the DR4 and basically have to start over and relearn everything since I only use it maybe once a year.
Tape over the cut areas can help a bit.
Also surprised you didn't use a TS to cut the grooves, for me, cutting long grooves with a tiny router bit is all white knuckle all the time 😱
Final box looks A-1 however 👍
Is this going to be faced veneered, solid wood, or ???