You may be looking at a range of $1500 to replace the tank to $20k for permits and relocating the leach field.

The second unit has its own USPS address, gas, electric meters but the city is unable to find  permit for it. 

That includes everything needed for permitting and plans ready to give to contractors.

@Andrew Bissada often you have to get the property under contract with an inspection contingency that will permit you and your contractor/inspector/handyman or whoever you want to walk and inspect all the units in the property.

The firms focus is in commercial property and I have learned an incredible amount about navigating city and county regulations, dealing with complicated leases, permit running and expediting and so much more.

You can build/remodel your own home without a license but obviously permits are still required and subs/specialties will need to be licensed.  

@Bryan Noth when you say holding cost, it’s time I’m not occupying the lot because of waiting for permits?

Permits and drawings are all approved and newly highly vetted contractors are ready to go.

You've got some major hurdles that will be quite challenging as a 1st time DIY project, and you will need licensed professionals to sign off on some things for permits: Structural (determining whether or not the wall you want to remove is load bearing and if so engineering a header and determining the framing layout for the new wall/door) Plumbing work will require a licensed plumber to pull the permitAny electrical alterations should be done by a licensed professional, a master electrician will be needed to pull a permitThere may be certain steps that you can DIY, such as GCing the project, demo, framing (following an engineer's drawings), sheet rock, tile, installing new fixtures/appliances, finishes, etc. but for the 3 big ones above you will need to bring in licensed pros if you're going to pull permits (which you definitely should).

To turn a garage into a legal unit you would need proper permits and inspections.