Tom, You can ignore the yellow error about the 1120 and file the 568 on its own. I don't know if the CA LLC 4/7 can be e-filed with the return. Doesn't that get filed with the SOS?
Does it say what federal form needs to be attached?
I've done several last year, just the 568 and it went through fine. Is question U (1) (page 2 form 568) answered "yes"?
There's some sample letters here if you absolutely have to send something:
http://www.cpai.com/business-insurance/professional-liability/ThirdPartyVerificationLetters
I use "Zzample" as the last name in the template files so they show as the last ones in the return manager, or you could use something beginning with "Aa..." if you want them to show as the first ones in the list.
I haven't had any speed issues with the software this year, but in the past the anti-virus program I used (McAfee??, I don't recall), would occasionally cause my system to slow to a crawl.