I would agree on a rate per hour for structural repair time and then add materials. In these cases no one can tell for sure what the job entails until you get into and under the old stuff.  Be there and see that they are in fact working diligently and using good replacement materials. Now is the time to fix structural problems.  What it costs it will cost.  As far as quality of the work, don't be afraid to speak up if you see something not right and discuss it with the owner of the company before they proceed.  You can not be squeamish about speaking up on a construction or remodeling job. They will hopefully figure out you are not going to accept shoddy work.

Good luck.

Jim at Dawn