If you download the latest source from git:
https://github.com/FrodeSolheim/fs-uae - then you should be able to compile with --disable-cpuboard --disable-ppc again.
Note, I'm not going to do anything about the PPC/PearPC code. I cannot even test the changes. But making that bit compile would as I said make it more likely that the next development versions work out of the box as I don't really use --disable-cpuboard --disable-ppc myself.