All our stumps are viewed and a price quoted. Because access and travel can vary significantly, by the inch pricing can be a problem. Also, as has been debated several times, by the inch pricing does not account for the volume to be ground as it grows exponentially while the stump diameter grows linearly.
Give a separate price for hauling mulch and a separate one for soil and seed.
eg
Grind stump x" deep - leave mulch $XX
Haul excess mulch - leave level $XX
Remove mulch to 3" supply top soil and seed $xx
Base you bid on estimated time and your hourly rate. You will need to determine your hourly rate (labour, insurance, fuel, equipment costs etc). Therefore it they want surface roots traced, then just account for it in the time it takes to grind. Same as tough access, just account for it in the grinding time. You should charge the same hourly rate if you are grinding or raking. And unless you like driving for free, include travel time.