I also have the applicant sign the application which states that lying is an automatic disqualifier, and the application fee will be retained for the work put into verifying the application.

It also gave me a good idea of ALL of the charges.I would like to find one that has a little skin in the game, to find and retain a quality tenant who takes care of the place and pays on time.

Rates will go up, keep your refinancing obligations in mind as well as your income, watch those debt ratios and retain equity so that you are not overly leveraged, otherwise, have a great exit plan. :)

Now I tell them you will need to give 20,000 upfront retainer and I will give 20k credit back off of your first deal.

Your purchase offer should explain who is holding the earnest money and under what conditions it will be returned to you and what type of account it is held in and whether that is interest bearing or not and who retains the interest on the money.With future offers it would be better to put under the earnest money section (upon written acceptance) in the purchase and sale offer.

For example I don't know if people typically pay some kind of retainer up front or only pay when they have questions.

Which could have been easily discovered by yourself, by contacting a title company or maybe the HOA itself would have been forthcoming.Now, if you contacted or retained a buyers' agent, these are just some of the duties the agent should be doing on your behalf.As far asking questions several times, that's not a problem.

I am trying to sift out the slag and retain the golden nuggets. 

Retain the services of an attorney who specializes in landlord-tenant law for your jurisdiction.Did you mail a letter of introduction to the tenant?

Here is so info on documents you should retain: http://www.irs.gov/Businesses/Small-Businesses-&-Self-Employed/What-kind-of-records-should-I-keep