Once it is up and running it runs great, only when it cools down (for example over night) it won't start.

Have you checked to see if the glow plugs are working ?

These links may help:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-8.html#post1415281

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-10.html#post1985158

@ Calif no I have not checked that... I should have added that I have changed fuel pump and both fuel filters, got new batteries... Still the problem is happening