It's a fantastic tool that yields information obtainable no other way with wonderfully precise timing resolution. It's just such a pain to connect 50 or 100 leads to run an experiment. In digital systems most of the analyzer's leads will go to the address and data buses. Build a standard connector you attach these to. Avoid wire-wrapped prototypes.
Digital designs are simply too fast now.
The PCB will eliminate all of the noise uncertainly inherent in a wire wrapped design. Go with PCBs from the outset. A misspent youth of blaring rock 'n roll left my hearing somewhat impaired, but helped formulate, of all things, my philosophy of troubleshooting digital systems. What makes you think ground goes to the chips - when a single part has 5 or 10 ground connections, make sure all of them are connected. The PCB may have manufacturing errors on internal layers.