My Toyota has that exact problem although it is an L-Jetronic based system. I have researched it for 11 years and all anyone can say is that it is a "hot soak" problem. Others report it but no solutions. In my case it only occurs when car is fully warmed up after 30 minutes of driving and car is stopped for more than 15 minutes but less than 45 minutes. The only theories I have developed are 1) fuel in rail boils or 2) some heat sensitive electronic component (coil?). In my case when it is running rough it has a very rich smelling exhaust (gas smell) and being a 6 cylinder I can feel as one after another cylinder comes back "on line" until there are 6 and it is smooth again. If I leave the hood up after stopping it prevents the problem. I have experimented to see if it was leaky injectors causing flooding and that was not the case. The unburned fuel smell does make me suspect the coil or some sensor.

Mike

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1998 C230 330,000 miles (currently dead of second failed EIS, yours will fail too, turning you into the dealer's personal human cash machine)
1988 F150 144,000 miles (leaks all the colors of the rainbow)
Previous stars: 1981 Brava 210,000 miles, 1978 128 150,000 miles, 1977 B200 Van 175,000 miles, 1972 Vega (great, if rusty, car), 1972 Celica, 1986.5 Supra