OP, next time it happens take a look at the overflow tank and see if fluid is getting dumped into it.
As the system loses pressure as it cools down it starts sucking coolant back into the cooling system (opposite as when it heats up and purges extra coolant). This is why it's important to use a Honda OEM 1.1bar cap.
By the way, you most likely need a temperature gauge sending unit. It's under $30 from Honda (only use a Honda one, I have an aftermarket and it's not accurate at all) and it's located under the distributor with a single wire lead. There's a similar sensor (ECT, engine coolant temp sensor) near it so don't get them confused. Coolant needs to be partially drained (1/2 gallon or so) to change it.
How did you check the thermostat? Place it in a pan of boiling water and watch it open?