"Scan tool", and "Cheap" are never found in the same sentence unfortunately, haha.
Some other things to look at from some google searches of your issues...
1) fuel pressure regulator could be acting up when warm. This would cause normal operation until it gets heat soaked from running, then it could start causing unregulated fuel to increase spikes or not allow enough through. Having a gauge on the shrader valve will be required when it's acting up to get an idea if you're having spikes or drops and when.
2) Potentially vapor lock. I know these boats have had issues with this. Does your problem occur only after you've shut the boat down, then restart? If you went out and ran the boat constantly the whole time, you likely wouldn't experience vapor lock. You WOULD experience vapor lock if you drive a couple hours, shut down the motor for 10-20 minutes or so, then start again and experience the problems then.
3) Bad distributor assembly.
4) Bad ignition module - these can heat up and start sending bad signals if they've gone bad.
Start with the cheap stuff, but there's some ideas.
-Mike
2006 Supra Sunsport 20V