So, no big news to anyone, but you should separate your network into backbone/distribution and access layers.
Layer 3 Distribution layer limits effect of spanning tree to a logical segment of the network. Limits the failure domain.
Cookie cutter configurations for client blocks and distribution layer routers. Symmetry everywhere – no exceptions.
Old tech support triad: Isolate, diagnose, resolve. Resolving the problem, once you have isolated and diagnosed it is usually trivial – a few seconds. It is the other steps that take time. If we are shooting for 99.999, a well-structured environment like this helps with the isolation and diagnosis steps.