Microsoft Money will allow you separate taxable from non-taxable items. When you mention "repair labor," I'm assuming that you are referring to your billings for hours. Without fully understanding your financial situation, I can't say for certain that Microsoft Money will be able to manage your repair labor, but it should. Handling parts is an area where Microsoft Money may fall short of your needs. If you are basically buying parts, adding a markup and then selling them, the program may be able to handle your needs.
Anything beyond this, for example, assembling parts, may be beyond the
program's capabilities. You can separate taxable and non taxable expenses in Quicken too. I tend to still do this on my own.
I create a report and then copy that report and paste it on MS Excel. From the Excel worksheet I then delete non-taxable expenses. This may seem like busy work but often tax expensable items are by category - hence, the report.
The report pulls together items you may purchase using a number of accounts. The reason I don't simply save the Quicken report is because if I want to manipulate the numbers - find an average fuel expense, for example - I can't do that with the Q report but I can in Excel.
I'm assuming MS Money has similar report capabilities. But I would never rely on a program to tell me what was expensable and what was not. The IRS isn't going to go after MS if I make a mistake