The common issue is that you are not calculating the sales tax as one figure. You are actually breaking it out and calculating per code and not per schedule. For example say you have a schedule that is made up of 3 codes, state, county and city. You multiple the order total by the state rate, the order total by the county rate and the order total by the city rate and then add them all together rather than multiplying the order total by the total rate.

I have already reverse engineered the tax complete calculation function. What I really need is the way the totals are calculated.

Not sure where your confusion lies?

sum of taxable items from lines tab  - discount (pro-rata) =  taxable sales

sum of non-taxable items from lines tab - discount (pro-rata)  = non-taxable sales

order total = taxable sales + non-taxable sales + freight + sales tax = order total

order total - deposit = net order