For the mouse try adding
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hint.psm.0.flags="0x3000"
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to /boot/loader.conf. For usb in general look at /etc/rc.suspend and /etc/rc.resume. I added an 'ifconfig ... down' statement to rc.suspend and reset in rc.resume. If it's only one or two devices something similar may work.
Changing the irq settings in the bios may help. On an older thinkpad I've set them to auto, the default was 11.