The Bayfront project and University make West Chula Vista interesting.

For example, their rent is $2000, they pay me $1000, I then apply the $1000 to the renovation project, which they estimate to be around $8,000.How should I write up the lease agreement as far as collecting the rents?

You can basic info on short term rental projections and occupancy rates with a free account, but will have to purchase a membership to get detailed info. 

In the end it's my responsibility to forecast any big projects that may happen in the next few years and make sure I'm covered for those.

Just ensure that the projected rental income comfortably covers the new payments, including the HELOC.

All this fancy mumbo fha guideline gumbo means is that your projected market rents assuming all units, if it were rented Times 75% need to be greater than what your monthly payment is  (PITIA = principal/interest/taxes/insurance/assessments monthly), other wise FHA will not lend at that loan amount so common solutions to this when rents are too low in your local market are to put more money down payment which defeats the whole purpose of low 3.5% down FHA doesnt it?

They then use their new knowledge and skills to take on bigger projects which they then BRRRR to scale more aggressively.I don't know a lot about North Carolina but I know there's investors there seeing great success. 

And then of course you have the 27 Boise Cascade projects that were built in CA  with thousands of lots in each one..

How are the performances different than your projections at purchase?

What's not going to happen is your going to get good long term pm done for you in rough areas with no other incentives like they are making money more on project management of the renovations.