All the Lufthansa or United flights from San Francisco that I can find arrive at the new wing of Concourse Z (gates Z50 - Z69). So far so good. If so, you will just go to the root of the concourse, find immigration (passport control), go through, then downstairs to the A Concourse. And most of the flights to Zagreb I see leave from an A gate.

However, I do see some anomalies. Gate A2 might be a waiting room for a bus that goes out to a plane parked on the Tarmac. And, I do see a B gate listed for a LH flight to Zagreb. In that case you will have to go to a different building, B. From the A concourse, there are only two options to get to B, and they both involve going outside security. There is a tunnel between A and B, but I think you have to go through security to get from the tunnel into B. Same with the SkyLine. You can board it from A, but I think when you get off at B, you'll have to go through security to get to a gate. The SkyLine (at least the Schengen side) is considered to be in the 'public', outside security, part of the airport. You can come into the airport off the street and get to the SkyLine without going through security.

If you stay on the Z (out-or-Schengen or transit zone) level, you can get to the SkyLine and go to the transit zone of B without going through immigration. I don't know whether you can get into the B transit zone without going through security, I've not been able to get anyone to tell me, but that's you only chance to avoid security going from Z to B. So once you get to the transit zone of B, you can go through immigration there to get to a Schengen gate in the B concourse.