he lets me call him whenever and gives me any advice i need and is super honest and will tell me what to do to make the most money even if it means giving up a deal he could easily pay me way less for. hes definitely someone who will play a huge role in my career to come flipping houses.

,I'd modify that to say that conveying title to your entity without the full sale and transfer opens the possibility of the lender exercising their rights under Due-on-Sale.

Regarding things that aren't written, you're not exposed legally but it allows the person you're dealing with to exercise actions that may better his position on your expense since there was nothing in the contract that had explicitly explained the situation.  

I'm new to the role of investor in Real Estate development, but I've been helping clients add value to properties for quite some time now as a Registered Architect.

The fact that the tenant exercised their option much quicker than you thought/planned is part of the explanation of your intent. 

Limited partners who only contribute capital, or several general partners with clearly defined roles?

I would create specific list of roles and responsibilities for each partner in the deal.

It seems like it is an exercise in language and at the same time getting the message across.  

John wants absolutely nothing to do with the rehab, and wants us to manage everything from finding the property to running the numbers to marketing and selling afterwards.I'm confused about the role of an investor in this case.

When you go sell yourself, the same thing will happen, except the roles will be reversed.