Newbie to RE investing but as I own a  small business my current accountant doesn't understand real estate and has been late in filing my taxes the last couple of  years.    

It doesn't mean that the or appraiser will agree with you!

What it doesn't include in an unemployed person sitting around all day running a space heater. 

This doesn't even begin to account for all the time spent and the high levels of stress that are inevitable when you're involved in litigation.I always tell my clients I don't want to turn away money, but there are times when it's best to just take a small loss and move on to the next deal. 

The market here doesn't seem to appreciate fireplaces anymore as most have Central H & A.

You might check out Podcast #60 or check with @Dave Van Horn directly if that doesn't answer your question

While it's better to do that than lose money in an area, it takes time and doesn't move the needle.

If I buy a 3 bed home for $200k, put $20k into it, the ARV can be $225k or $500k, it doesn't matter.

The other concern I have is that at least in California, it's important to do everything by the books that way a tenant doesn't have the opportunity to come back and say "but that's not what you did last month". 

Doesn't the city permit office make sure the property is repaired correctly...to code...apart from the smell?