MacOS – Mad Catz R.A.T. 3 mouse problems on MacBook Pro

Based on the information provided I would say the mouse settings are not been loaded.

You can add the "MicrosoftMouseHelper" to the log in items area.

That should override the OS X defaults.

The file should be located in your /Library/PreferencePanes/Microsoft Mouse.PrefPane/Contents/Resources/MicrosoftMouseHelper

You can check which processes are using the most time interval in the system calls:

sudo fs_usage | grep -v 0.0000

^{See: How do I debug an out-of-control “kernel_task” process?}

In case your macOS experienced out-of-space scenario, some services can be still in a freeze mode (causing some freeze timeouts) and they need manual unpause by the following command:

kill -CONT -1

Otherwise check whether clean restart helps with anything.

If you had any unexpected shutdown after freeze, it's good to check for the shutdown code.

If won't help, if you experience another freeze, hit ⌘-⌥-Control-Shift-, (Cmd-Opt-Ctrl-Shift-Period), this will trigger sysdiagnose process which will quickly gather system-wide diagnostic information helpful in investigating system memory/performance issues (will appear in /var/tmp). If you're technical person, you can consider uncompressing the generated file and analyse the logs, or contact Apple support if they can help you.

If you believe you've a virus, just install antivirus (such as Sophos Home) to exclude that. But having antivirus, can cause another extra freezes as well, so it's up to you.