Double check with your local building department before you enter into an agreement with this guy, but based on the info you provided it sounds like he will be allowed to do it.Keep in mind that if your design includes elements like trusses, lintels, oversized wood beams, etc. it will probably need to be stamped by a licensed engineer, regardless of who drafts the plans.

I was aware some of the stone and brick needed re-pointing when I put in my offer, but the inspector found some deteriorating wood beams that are of real concern. 

The main structural beam is being replaced so I am using a licensed contractor.  

If you take in all that negativity or warnings, and are still laser focused on this DESPITE all the dangers, well that right there may be the BEST indicator you got the chop's for this!       

I have really been having some thoughts about am I still doing what I’m supposed to be? Am

I have one of those laser measure tools and do it on inspection day.

Zillow absolutely, 100%, is laser focused on completely re-defining the transactional process of real estate in the entire United States, no joke.

Become laser sharp focused with one specific strategy, run your numbers based upon your learnings, have a seasoned investor check to see if you missed anything significant, and maybe choose a "not so expensive" property as your first attempt.... 

Has anyone poured a slab in-place of an existing pier and beam foundation? 

I like this better than all wood.The beams and bead board ceilings still give it that cabin feel.I think it will do great!