I'm not opposed to setting up my books properly from now on, but am afraid it combined with the late filing will trigger an audit. 

Being laid off, meant NO money coming in, and there were NO jobs requiring help.Dad filed for unemployment as he had done in the past.

Or if your intent is to force a separate tax filing so it’s not on your personal 1040, then he needs to be involved at the very top level so that your business returns flow into the final LLC to generate a k-1 to your 1040.That’s my laymen’s two cents

I’ve filed for my first LLC and plan to quit claim deed into this entity after the loan closes.

In a slightly more specific manner, I don't really keep a "file". 

You could just make it simple and collect rent to offset your cost of owning and not file all the extraneous baloney, then convert the whole property to business rental when you move on.

I live in California and have property in Detroit … my question is do I file taxes in Detroit solely for my properties?

Daily photos should be included in your contract and sent to you daily for your file.

If this dude can't complete your projects....you definitely aren't collecting from him if you somehow won the case.Then you'll be out even more time and money...Forgot to add, you're most likely bet and efficient use of time is to file a complaint the license board for the state..and if you're using an unlicensed contractor well you really have no plausible recourse through legal channels.

Ask questions, keep a file so you can compare, and don’t let each lender pull your credit until you decide on the right product for you.