MCT
According to ExpertFlyer, it should be a legal connection:
STANDARD.D/D...D/I...I/D...I/I.
ONLINE 1.00 1.15 1.45 2.00
OFFLINE 1.00 1.15 1.45 2.00
I can't get it to work using multi-destination search either -- unless I add in a bogus third leg back to FRA, in which case it comes up fine. You should be able to call them to book it, and if you tell them that you couldn't get it to book via the website, they should waive the phone-booking service fee.
Regardless, you may run into issues getting that award to price properly. In theory, you should be able to use a single business saver award provided that business saver or coach saver is available on each leg. In practice, the computer doesn't always seem to price it correctly and it may add the award amounts together.
Note that your connection time at JFK can be as long as 23:59, and that you could connect using another partner (e.g., AC), so you have options beyond the p.s. flight.
Having said that, if you're going to SFO anyway, I'd look for FRA/SFO flights on the A380. Of course, I can't promise LH will release any seats... :-)
Regarding your original question -- I would not expect UA to accommodate you in case of IRROPS if you're on two tickets, even if they're both UA tickets. They may do so, but it's not a requirement, so you're depending upon the agent being in a good mood.
Enjoy your trip!