Haneda airport transfers to Hiroshima

We are flying Qantas to Haneda arriving 6 am and considering a 9:30 or 10:30 flight to Hiroshima with ANA. Would this be enough time to get to the next flight ? 2 travellers with checked luggage. Would we clear customs at Haneda or when we arrive at Hiroshima ?

Should be enough time. Budget around 1 hours for immigration and customs at Haneda, could be 30mins.
https://www.japan-guide.com/forum/quereadisplay.html?0+177850

QANTAS and ANA are two different company. Did you book you flights together?
What did the travel agent said ?
considering a 9:30 or 10:30 flight to Hiroshima with ANA.
But then again above statement seems to show that you have not made any booking for flight yet?

You are flying from International, so you will clear immigration/customs at Terminal 3 Haneda.
You will then need to transfer to T1/T2 depends on your domestic flight.
https://www.japan-guide.com/e/e2430.html
https://tokyo-haneda.com/en/
T3 is Arrv/Depart for international flight. T1(JAL)/T2(ANA) is for domestic flights.

You will clear customs at Haneda Airport and then transfer from Terminal 3 (International) to Terminal 2 (where ANA's desk is located).
3 and a half hours seem okay to me, but please keep in mind that changing terminals at Haneda will require using a connecting bus or monorail. Additionally, if many other flights from different cities with a massive number of passengers arrive around the same time as yours, you may need longer waiting times at customs.
According to Haneda Airport's website, flights from Bangkok, Singapore, Delhi, and Shanghai are scheduled to arrive at Terminal 3 around 6 am, other than Qantas.

https://tokyo-haneda.com/en/flight/flightInfo_int.html

Having done more stupid early morning pickups at that time than I would like, an hour for processing and either train to T2 - you should be fine.