I did a similar rip and replace - I ended up using CIDR on each side of my core links to remove layer 2 vlans traversing my uplinks - set my root on each side and it's running much better now - I struggle with no pvst - I did set my cisco switches / stacks to mst mode but that did not resolve my issues. I don't allow all vlans across any trunks, I only allow the vlans that are needed - I am always very careful about having the same settings on each side of the link. I miss not being able to do "no spanning-tree vlan#" .....
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