There is WAY too much to cover in this thread....from the actual landscape job and customer-purchased materials (YIKES) to the pricing issues.
But the rental equipment thing stood out to me. Why wouldn't you itemize a piece of rental equipment in the estimate?!!? Example: We have a Dingo, but not every single attachment and if we need the soil cultivator attachment on a job, it gets in there for XXX.xx per day under "machine rental".... part of the cost of doing the job and the customer has every right to understand that.
What's the issue?