I would be very careful about the laws of your state/city if you are renting it out as a air bnb you could get into trouble depending where you live.I did a quick search and I found this https://www.charleston-sc.gov/1520/Short-Term-Rental-Ordinance-Process do you have a short term rental permit?

Of course by a license contractor with the correct permits, etc.My main qquestion is, since there is going to be an additional tenant should I decrease the rent by 5% for the current tenants?

Usually, if there is a public utility line, this would be disclosed to you during the permitting process.

How difficult is it to get permitted for a multi-family when the property is zoned RS40 land use description "single family"?

I’ve been reading a lot of old posts about pulling permits and the general consensus is always pull permits when required by the city/county.

Current site plan attached uses the existing building and permitted construction drawings have raising the roof and a whole new facade with a drive thru. 

Get building/reno permits- they are Cheap and in CA code inspectors will be on site within 24 hours of the request.

The violations include pulling construction or electrical permits and the fines are seven figures.

That basement would be awesome if permitted to bump the ARV and add value.....  

I have asked standard documents through my attorney to the seller's attorney - leases, insurance with any claims in the past years, service contracts, any permit violations, etc during attorney review.