When the ground is excavated for the slab and footer, they will also have to remove the remnants of the tree. Roots that are deeper than they need to excavate won't be a problem.

The per-square-foot cost is what you calculate after it's built. Too many variables. You'd do best to get a design, get it reviewed for code compliance in your area, and then get three bids (after researching builders in your area).

I'm commenting to follow as we are interested as well (though we want an apartment attached on the side, not upstairs).

The GC will be required to build the garage if it is in the original loan documents that were bank approved. It would not be allowed to be built by a third party not under the control and supervision of the bank approved GC. If you or the Amish gentleman have a contractors license and insurance, the GC can certainly subcontract that portion to you, and you can build it. If the GC agrees to that. I would not plan on that happening. If the GC would take on the liability of hiring you as a laborer under his workman’s comp, then he could do so, and instruct you as an employee to build the garage. I would not plan on that happening either. Free liability is a hard no thanks. In all situations, it is the GC that will need to be paid by you via bank disbursements for building the garage, as that is the professional that the bank approved to be responsible for the build. The bank has not approved you to be involved as a co GC, or to work on their investment, or to hire whomever third part. All job responsibility goes through your GC. You are the funding conduit between the bank and the GC as the owner only. You don't ”recoup” cost overruns. Those are expenses that add to the COST of the build, but not the VALUE of the build result. They are spent and gone. Your savings account is permanently depleted until such time as you add to it again. If the bank agrees to reimburse you for the documented overruns, then you will just have to pay it out all over again when the specific loan amount runs out, and the project still needs that money to reach completion. If you do manage to cut build costs somewhere , that does nothing for your savings account. It does affect the loan amount. Cutting things also affects the value of the house, which will likely require a reappraisal and redo of the loan. That will require you to bring more cash to the table to cover the value shortfall. This is a shell game that only the bank wins. You always end up out the extra costs.