However, combining them creates problems that will be difficult to overcome.Let me explain further.  

Rarely one finds appreciation and cashflow in one single deal.

@Abraham Anderson finding a value add deal that sells at a true 8% cap (actual not proforma) is very rare in a hot market like today. 

I know people have found great success in all kinds of REI, but his primary argument is that buying a good, normal home in a good neighborhood will provide the highest appreciation rates, which combined with leverage is the real wealth generator.So imagine a hypothetical B class neighborhood that has both small multifamily and single family properties.

This is rarely the case, so I think you know where I'm going with this.

The reason the rent is low compared to the value of the property is a combination of the local economy as well as the type of property.  

Very rare right now. 

The fact that it's some combination (3 out of 4) of an ARM, crappy interest rate, points up-front, and larger down payment, will give it away. 

Is there a way to combine these into one loan and document it all with a single mortgage and promissory note?

Rarely needed and only increases investors costs.