A couple of things..
It is very common to NOT have a dedicated root aggregate on smaller systems. A dedicated root aggregate is not a requirement in 7-mode. Not having a dedicated root aggregate does not limit functionality in any way.
The multi-tier VIF/IFGRP that you see is also very common in smaller environments that do not have stacked switches.
For example:
Ports e0a and e0c are part of an LACP bond with both connections going to the same switch (vif1)
Ports e0b and e0d are part of an LACP bond with both connections going to the other switch (vif2)
vif1 and vif2 are then placed in to a active/passive (single mode) LIF called "svif".
So at any given time traffic is on once switch or the other.
Without stackable switches, this is the only way to provide link aggregation AND switch redundancy. The flapping could be the result of a misconfiguration on the switch or the NetApp. We would need to see the /etc/rc files from the controllers to determine exactly what is going on.
In regards to the performance..
What does 'sysstat -x 1' show? Are CPU or Disk Util % high? I would consider anything above 75% to be cause for concern or at least a place to start looking.
If the network is flapping, I suspect this also may have something to do with the performance issues.