Including logging in, navigating, scanning in the mortgage statement, entering the transaction into my bookkeeping software - I can pay a mortgage in about 5 minutes.  

You can divide some of them out each year they occur - but only some and I find the bookkeeping easier if I don't do it that way. 

Don't forget about the 50% rule; as a rough estimate you can expect 50% of your collected rent will go to prop. management, advertising, covering holding costs, vacancies, repairs, advertising, legal advice, book keeping, insurance, taxes.

Late a couple days, OK, maybe he does it all and doesn't have a bookkeeping dept..

You then remit them to the taxing authority.As suggested, your best bet is to talk to your accountant or bookkeeper.

That does include taxes, insurance, maintenance (which is usually caused by the tenants so being newly rehabbed doesn't help), vacancies, any damage in excess of security deposits, make ready costs, utilities at least when its vacant, legal fees, eviction costs, book keeping, etc.

As we acquire more and more (mostly buy and holds, but also some rehabs for a quick flip) it's becoming more and more of a hassle to keep the books.I am yet to find an adequate piece of bookkeeping software which really lends itself to real estate investing.

All you need to do is account for them separately in your bookkeeping software.

Worked in property management, bookkeeping and realtor!!

We did this because it was great for bookkeeping and it didn't cost us any fees.