You might be having problems with Speculative Access. Basically, all modern CPUs guess what instructions might come next, execute them, and then keep or discard the results. This is a problem when the CPU guesses I/O instructions that change the state of something, and G3 upgrades in Old World Macs tend to make these bad guesses. The symptoms are random stability issues, data corruption, and failure to boot.
Fortunately, someone made an extension called ROM Fixer which disables Speculative Access, and I found a copy on the Wayback Machine (also attached to this post). In my G3 upgraded 9600, this solved all my problems except the occasional failure to boot; the three-finger salute gets it going after one or two tries. I have the extension installed in both System 7.6.1 and Mac OS 9.2.2, and it's probably compatible with every version of the classic Mac OS a 9600 can boot.