California charges a minimum tax of $800 a year per LLC, and more if you have gross receipts in excess of $250k.

I will honor my agreement of refinancing or doing a loan assumption as soon as I'm able (I've been trying excessively over the past decade), however if he does force a sale, can I tack on the fact that I've paid all expenses including the mortgage for the past now 13 years to demand he reimburse me half, or is he entitled to half the equity and I'm just screwed out of everything I've put into the house?

You may need to play around with how you word your request, so you won't get charged for an excessive amount of pages. 

Would it make more sense to live in old side and work on it while living there and still make rent on other side while losing out on being able to claim expenses as tax deductible or live in updated side and loose out on rent for about 4-6month(1300/month) but be able to claim all expenses as tax deductible.

There are lots of ways you could do this, but the execution is largely up to you.Most of the private lenders I have worked with were experienced real estate investors themselves with excess cash they wanted to put to work. 

You should only consider switching when your current software has a significant flaw or lacks features that force you to spend excessive time on workarounds.

The fact the taxpayer even has a w2 can cause an audit and one they tax payer will likely loose.

They are literally ten times better, more experienced and more professional than most of their peers - and will still loose out to a consumer who has a friend of a friend with little to no experience! 

Once tenants loose that buffer in their bank account to pay on the 1st of each month, they are going to struggle to keep up. 

Our first two projects were conservative by choice and combined yielded in excess of mid six figure return.