The additional payments I have been making on this mortgage are sure to be lost or discounted because of how bad their bookkeeping has been4.

Book keeping takes time. 

@Mike RomanoHave a third party bookkeeper and be transparent with all payments and invoices

It would also require IRS approval in this case to make this kind of accounting change.The bookkeeping will take more time, but on a good sized project it would make sense.

In a similar vein - do you personally use a bookkeeping software or do you do it within your financial institution's capabilities to help ease tax time? 

I have received a refund for a transaction that occurred in the previous tax year.
Specifically, this transaction occurred in May 2023, but I received the refund for that amount in January 2024. I’m struggling with h...

There's both bookkeeping and property management features available. 

Consider looking for a bookkeeper.

Anything that also helps you keep your bookkeeping in place?

Most people I talk to do it for book keeping purposes.In a recent conversation with one of our investors, she mentioned that she was encouraged to set up her own LLC for her real estate so that nobody can go after her investments if she is sued personally.