K0UA has some good ideas. Mac (Apple) clocks are usually correct, never had that issue, but with Windows yes.
MAKE SURE, I WILL SAY THAT AGAIN, MAKE SURE !!! that you read, the "read me" file that downloads with the program. You may need to do a few things to Mac OS using script files. Not hard bit confusing at first.
Then as said above, turn off the rig, REMOVE the USB cable and then reboot the Mac, put back the USB cable, then turn the rig off. You can always reload the correct drivers again, ( Mac not a fussy as Windows).
Check the Yaesu manual and see if you need a special USB cable, forget if I do use one.
Make sure your Yaesu menu settings are correct for Digital modes. May times that can cause issues.
All that being said, Yaesu rigs give me the bigger pain in the butt setting up things like that. My Flex 6500, Kenwoods and Icom are all easier.
The FT 3000 is getting a bit old now. You will find that all of the newest rigs easier for the newer modes.
If all else fails buy a MicroHam USB III interface. Will work with all rigs old and new ( will need cables ), and you will find the MicroHam software will allow you up to 30 virtual com ports and get rid of your menu issues plus it has its own sound card.
Once you get past the few nit picks of getting the Mac to work you will like it. I use it with my Flex 6500 , Icom 7300, kenwood 590gs, and kenwood 890S
If you are still stuck next week look my call up on QRZ and email me your number and I will try to call you.