"How do I delete the recovery partition from both disks if I'm cloning my HDD to the SSD?"
I'm assuming you bought the Mini with the 1tb HDD already installed.
In that case, it comes from the factory with a recovery partition on it. One way to get rid of the RP would be to re-initialize the drive. You might try this after you get the SSD installed. That is:
1. Install SSD
2. Initialize SSD
3. Use CarbonCopyCloner to clone contents of HDD to SSD
4. Boot from SSD
5. Initialize HDD
6. Use CCC again, this time to clone contents of SSD to HDD
The SSD will come WITHOUT any Mac-formatting. You can just initialize it as one partition. If you then "clone" the contents of the HDD (main partition) using CarbonCopyCloner, you can set up CCC so that it doesn't clone the RP as well.
IMPORTANT:
CCC now comes with the ability to clone the RP as well as the "main" partition. You must set up CCC so that this capability is TURNED OFF, if you don't want the RP cloned, too.
The reality is that if you have the SSD setup as your main drive, and use a part of the HDD to serve as a "backup clone" of the SSD, you no longer need a recovery partition, because you'll always have a second, fully bootable copy of your main drive close-at-hand.
"If I were to boot DU from a USB recovery disk would that still try to repair a fusion drive?"
Interesting question. Not sure about that. The only way to be sure, would be to try booting that way, but ready to pull the plug if things got too far!