We were running Workflow 3.4 and have now migrated to Workflow 3.5 sp6. Things went smoothly but we are now doing stress tests and we have some performance issues.
I went back and did additional reading through all the manuals and discovered that I had left out an option when running fmczm350. From the wf350sp6.enu file:

Use the utility with the following options:
fmczm350 -c -d -f -y XXX
where XXX is the name of the configuration.
When specifying -h you get further information about the
possible options. The option -f is new, and enables necessary database
changes with this service pack.

I didn't use the -f option. What does this option really do? "necessary database changes" is kinda vague.