Today I received a codes violation stating the lower units kitchen was not permitted. 

I am planning to use as recreation and possibly build a house on.

If you decide to move forward eyes wide open, then don't skip the permits. 

I'm trying to read up on pulling permits and recently came across this line:"Individuals acting as their own contractor must be the landowner, permit applicant and the person signing the application.

All require a permit/license.I would definitely point you in Arvada's direction, as they've just put updated regulation into place allowing up to three owned properties to be run as short term rentals. 

There are lots of great contractors out there - in Oxnard, you will be required to provide a City of Oxnard report, which shows all the open permits and closed permits for potential buyers.  

A lease also is not conveying the rights of ownership required to contract with others or pull  permits required.Leases can be terminated, bankruptcy, foreclosure, estate matters, law suits, or if an owner must move back into a property as their principal residence, can have a lease terminated.Review the concept of the "Bundle of Sticks" ownership rights and what a lease conveys, it is only the right of possession, not all rights.An option can also be broken, consideration may not be sufficient, it may be drafted improperly or illegally.

Even Toyota cars have had some very negative reviews.The big issues with those builders are that they do not get permits for you, you have to do it yourself, they do not have city utilities connected for you, you do yourself. 

Our architect was convinced that it was going to take at least 1-2 years to get our permits...we got them under 3 months.

I do not know a lot about real estate (as mentioned above) but I was in the outdoor recreation business at one point.