I try to set the vacancy percentage to what will come close to covering all rent on the year for one month. 

Would never choose a property manager whose sale pitch is that he can do it for less percentage than others.

Additionally, I'm finding it difficult to reconcile the fact that when you project 3% rent growth and 2% expense growth for 5 or 10 years, your expenses as a percentage of EGI (which should be around 50-55%) get way out of wack (40% or less).

We ere planning on using a property manager and just paying the $100 dollars or percentage of rent.

It is a small percentage of the purchase price, and it will give you the assurance that when you are ready to sell down the road that you will have no title issues to clear up.

In this way we will slowly raise the percentage rate of online payments as we turn units over. 

I think the profit margin percentages were 27%, 21%, and 8%.

If the monthly bill as a percentage of the cost is less than the rent as a percentage of current value then it probably isn't worth it.

However, if I am just analyzing properties quickly, are there any quick ways to guesstimate the expenses - like rough percentage thresholds for each expense category?

I have a manager that works for me for a small base salary and a percentage of rents and flip profits.