Have changed fuel filter and car will run but after driving it awhile and stopping to go in store it must set for 10-20 min then will start back up it just keep doing this

If the CEL comes on and then goes off after 2 seconds, when the ignition switch is turned to ON (Position II), then replace the Ignition Control Module (ICM) and coil:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-4.html#post265896

The ECM Backup Fuse is located in the under hood fuse box--usually 7.5A.

Check engine light comes on sometimes when driving and will go back off but when you start up again it will comeback on and like I stated earlier the car will have to sit 10-20 minutes before it will start up again this is confusing me because the distrbutor and fuel filter have been changed.it seems like once engine gets hot I have this problem.

If the CEL stays on, when the ignition switch is turned to ON (Position II), the ECM is likely failing--very common on older Hondas.

Car refusing to start after being driven once you stop must sit 10-20 minute before starting again have changed distributor and fuel filter and sometimes the check engine light will go on and off while riding or turning key on,if anyone can help I will sure appreciate it because I am very confused.

Most likely possibilities are the ECM or main relay. Perform tests, in Honda Sections 1 and 2, below:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563.html

It's common for cold solder joints on Honda main relay PCBs to separate, when they heat up, and the car won't start. In the cool of the morning, everything is fine; however, in heat of the day, the engine won't start. If this sounds like the problem, just replace the main relay--some people try to resolder them.