You don't want to disturb the soil around old clay pipes unless you understand what your doing.A camera will tell you if its iron or clay and the condition of the pipe.

We hired a soils engineer that did all the compaction testing, etc. and updated the soils report that came with the land. 

According to me the tree is saving you against many things like heat, Soil erosion, UV rays(there are many more pros).

I was attempting to shut off my water valve from underneath the sink in the bathroom, however I learned that the shut off valves no longer work.

Proposal: Our recommendation is to; -Excavate, remove and replace outside cleanout with pvc to proper grade-Tunnel underneath the foundation from the outside near the cleanout, removing hazardous waste, dirt, and old cast iron sewer pipe-replacing cast iron pipe with pvc with proper grade to meet all sewer ties, back filling with sand and dirtThey estimated 12k in plumbing work, with the following statement "Any siding, sheetrock, flooring, etc. removed which is necessary to the repairing of the sewer will be put back by others."

Contaminated soil is an issue.

Do you have a team in place, architect, civil engineer, soils engineer, general contractor?

Which architect are you usingWhich GC are you using Are the soil reports done on the property already or is that another cost and variable you are unfamiliar with What kind of material do you want to use I can go on but I'm sure you get the idea. 

I know they are insanely expensive, but a septic system that is effectively a waste treatment plant can function in almost any soil.  

My solution, is we make our properties as indestructible as possible, tile flooring throughout and we caulk like crazy to avoid it getting underneath.