The 8Gb in use by mysql looks to be your problem. We only have 500 agents and mysqld is using over 9Gb of memory. Logic would imply you should be seeing something more along the lines of 25Gb in use by mysql alone.
I can't supply you settings for your number of agents but there are a fair number of postings in this forum on sizing mysql, with examples. I'd recommend starting with a default my.ini, apply the changes recommended in the CW docs and then apply the changes people recommend for similarly sized installs. One change at a time so you can roll back.
I've attached my my.ini, wh