If there is a property management company involved, I would feel more comfortable.

Very comfortable with cold calling and being told "no" by prospective buyers. 

You are making the investment so you should be the most comfortable and most in control of making that decision.

What are some practical steps I can take that will ensure I get comfortable with “running my numbers” and ensuring that the deal is in fact a “good deal”?

There are a ton of different ways you can go depending on what your long term goals are and what you are comfortable with.

Lots of people are OK with that because a lot of times people buying in that 2 to 5 million dollar range are more "sophisticated" than someone buying their first home or investment property and they know their way around the deal and don't need guidance, they just want to get the deal.If you feel comfortable with the deal process and economics then I wouldnt worry about what the listing agent is going to earn but if you are worried about getting hosed, you probably should be and hire an agent to work on your behalf.

So if they feel good to you other than this, I would feel comfortable renting to them....

Lesson learned, don't sign until you are comfortable.

I would hit the board and narrow down how much more you would be willing or able to spend and still be comfortable if you found a higher priced deal that is more wholesome.

But just make sure that your VA can be trained to run numbers and comps so you could maximize your time and dedicate it to close more deals.