SJC Controller described operational deviation when clearance readback was missed; reporter claiming distractions and poorly located run-up area.

Narrative

P28A contacted Ground for taxi without a clearance. Since it wasn't busy; I issued the appropriate VFR clearance and instructed the pilot to taxi to Runway 29. He read back the instructions correctly; and then short of the runway turned askew on the taxiway; apparently doing a run-up. (This is not the proper location for run-ups.) To get the pilot out of the way for other aircraft potentially exiting the ramp; I said to the pilot; 'The run-up area is actually across Runway 29. Hold short and contact Tower 120.7.' The frequency I issued was the Local 1 position; and not the correct frequency for the current Tower configuration. The Local Controller turned and told me I was giving the aircraft the wrong frequency; and at the same time; the pilot was reading back the previous instructions. He said 'Taxi across Runway 29 and contact Tower.' Because of the interference of the Local Controller; I missed the readback; and the pilot crossed the active runway. There were no aircraft inbound; and no other aircraft taxiing at the time. I observed the pilot crossing the runway and asked the Tower if they had crossed him. When the Local Controller replied that he hadn't; I said there was a possible pilot deviation; and only when we listened to the tapes did I discover that I had completely missed the readback when I was distracted. The poorly placed location of the Runway 29 run-up has been the source of several pilot deviations as well as controller deviations. Contributing to the deviation was poor phraseology on my part; and distraction in the Tower.