But not till the best applicant has given you a deposit and you have signed lease.. 

If anyone has a certain contract that they have used before, that is applicable, that would be great.

Another option would be to consider a property management software suite such as Buildium - I use if for everything from application to tenant screening to accounting, document storage, and tracking of maintenance requests, and could not function (or scale up) without it.For example, if a tenant enters a maintenance request, I can turn that into a work order, assign it (and email it) to a contractor from the system, and then pay the contractor via EFT or check out of the property's rental income (if desired) when I close out the work order.

My plan is to put together a PDF folder, with every PDF document that I will need for every time a tenant moves in, listed in order, including things like a minimum qualifications list, rental application, denial form, acceptance form, and so on, all the way through the lease, and handing over the keys.

This means you will get much better tenants and people who want to stay.I actually rent right at and sometimes just below market rent to attract better applicants as well. 

Also, does any one here at BP know of any other similar applications or software?

Charge tenant $40 or $50 application fee.

The banks will have their own metrics on what % of the income will be used for CAPEX/Repairs/etc and will do their own DTI analysis on the property stand alone.This should all be part of the bank loan application, they generally have an income/expense worksheet for each of your rental properties.

One collection doesn't seem excessive though considering we have had other applicants with higher frequency and dollar amount. 

I use a point system to rate applications.