with "OS4 for classic Amigas only supports main memory on the BPPC/CSPPC board (and chip memory on the motherboard)", are you saying that the RAM on the mobo is not seen by AmigaOS4 or that it will not starts?
when you will get the problem fixed (which i have no clue about why happens) rise the dosbuffers to at least 400, or you will get a lot a cache misses and then setup a good Read-ahead cache setup with SFSConfig OR SetCache
edit- here i'm not 100% sure but seems that the latest SFS versions are very sensitive to the identifier set in HDToolbox.
For some reason HDTB, doesn't recognize correctly the identif?er, setting it at CFS (Custom File System or so)