IMHO you should not ignore the possibility of a hardware problem. Because the problems started when you added another expansion it could be that this combination of expansions does not work well. Or perhaps you exeeded the limit of the power supply. Or the air flow is no longer sufficient to stop the system from overheating. Or you accidentally loosened something, for example the SCSI cable. The CPU connector is another candidate for loose contacts. The error indicates something related to corrupted RAM, so CPU connector, RAM connectors, Zorro connectors especially on the BigRAM are things to check. Heat is another thing which can cause this.
A corrupted harddrive or data corruption during read operations may cause such problems, but actually it's unlikely that the system boots up until WBStartup without problems if this was the cause.
Failure of AmiDock is usually caused by bad picture datatypes or wrong versions of gadget and image classes. After AmiDock crashed because of this reason, it's no wonder that other programs don't open, either.