The rentals should still be listed under Schedule E unless you are providing more than just a rental(Substantial services such as concierge services).You may want to interview a couple of accountants as this decision of schedule C vs Schedule E can make your return deemed incorrect and increase the chance of an audit.

Is it a reputable company and will the documentation provided from the study hold up in an audit?

Hospitality, attention to detail, cleaning/handyman team, programs used for bookings and calendar organization, inventory audits, home maintenance, etc. are all extremely important but all of that doesn't even begin to describe all of the things an experienced property manager does.It is a matter of how much time and energy you have to invest in your properties and if that time and energy is worth it to you.

Then, we meticulously log the hours in an Excel doc in the event the IRS attempts to audit us.

I wouldn’t recommend DIY—it’s risky and often not audit-proof.

Schedule C)- Preparing audit-ready documentation in case the IRS ever asks questionsIf the $4,000 quote includes all of that, it's a reasonable price for the value you're getting.On the other hand, if the CPA is just doing basic tax filing, and not helping you plan or qualify for tax-saving strategies, then $4,000 is likely too expensive.

Having this documentation is crucial in the event of an audit 

While separate accounts sure helps with the audit trail, it's not necessary if you note the reason for a a deposit and withdrawal on the drafts or "source" document. 

It sounds like I'm begging for an audit lol.

What matters is having the right setup and making sure the study is done properly (engineer-led, audit-defensible, etc.).