I am also required to submit an affidavit of continuous marriage.

You might want to get a pre-approval loan letter or a proof of funds letter to give you a better feel when you submit it with your offers.  

My properties are managed by 3rd parties and the accounting software is "baked" into the property management software.I don't know how big your real estate empire is but from my perspective, and as someone who is very skilled in Excel, my recommendation is that you find a good bookkeeper who is really good in Qbooks and have them assist you with setting up your company the right way in Quickbooks such as chart of accounts, categories, lists, etc.

Extended vacation was nearly a month, we submitted on July 17 and received acceptance letter on August 4. 

Before you submit an offer, do you have a single contractor (maybe your go-to person) walk the property with you and estimate costs to rehab OR Do you have a few different contractors walk it with you?

If requested, an organizer is very simple to print out from most professional grade tax preparation software.

The biggest gripe I have with the payment service they have integrated into their software, Forte, is that it is slow; it takes about 8 - 9 days before rent paid on the first of the month finally reaches my business checking account.Buildium is another PM software that automates rent collection, and it comes highly recommended by a number of other landlords at the REIA that I belong to. 

You can submit a lower offer or improve the building to increase the rents but that is all situational.

I came into real estate from a software (and consulting) job as well :-)Since you have your own house, maybe trying pulling a HELOC from it? 

This would also be relevant to their ability to post rent on your accounting software Or, have them mail it in and then you handle it or your back office .