Looking for advice in refreshing / recalibrating my setup

First things first. Make sure you read this and that you’re ruling out interference.

Next, the best way to start is to fire up your ZHA map and see what routes your devices are currently taking. If you see some routes which don’t make sense (like a router on the first floor directly connected to the coordinator instead of a nearby router), then you might want to remove that router and pair it to the other router yourself.
It won’t guarantee that the router will maintain that route, but at least you’ll know that if it starts routing via the coordinator again, the device is correctly selecting what it feels is the best route.

Second thing you need to watch out for is how many devices are connected to your coordinator directly. The Dongle-P page has some inconsistencies regarding how many direct connections it can handle.
The main product page says it’s 21 direct connections & 40-100 children via firmware update:

Meanwhile the FAQ section at the bottom says 50 direct connections & up to 200 children:

Either way, check if there’s a firmware update available for your coordinator, maybe that helps improve things.

Lastly, you don’t mention whether the groups you have set up are HA groups or Zigbee groups in ZHA. HA groups will fire multiple zigbee commands, one for each device, while a ZHA group will only fire a single zigbee command.
Switching to zigbee groups (if you haven’t done so already) will reduce the traffic on your network.

If all else fails, you have 2 options:

  • Have your automations repeat the command multiple times using a delay and a repeat.
  • Nuke your entire zigbee network and build out your mesh from scratch, starting from the ones closest to the coordinator and adding further away devices as you go along.