Welcome to the club. I still regret purchasing a Lion Server Mac-mini this fall. It took me many hours just to get my FM PHP service running again, and I don't really understand how I did it. I tried to get help from Apple's Server support people and they were not very helpful. I paid FileMaker for extra special help and did not get a clear answer there, either.
I (and other people; see the Macworld magazine review) feel that Lion Server is half-baked. Its documentation is inadequate and there are unexpected changes. Just today my IT director and I began discussion of downgrading our machine to regular Lion. We asked ourselves, why do we need Server is we just want FM Server and Apache/PHP? (I would prefer to just use Snow Leopard Server, but this newer Mac-mini requires Lion.)
My advice to anyone who wants to run web on OS X Server: Stick with Snow Leopard for now, if you can. Lion is not ready.
Gary, thanks for the reply but my solution was a reinstall of FMSA yesterday afternoon. It reinstalled the flavor of php that it needed and is humming along. I feel your pain on upgrading but this one has actually been great for us. ( except for the php issue, which was minor at this time) The features in Lion Server that were not in SL Server are right up our alley, but I do agree that documentation is a joke. All in all I have to say thumbs up!