Providing proof of funds BEFORE accepting an offer verifies that.

We thought that by hiring a company that's verified on sites like HomeAdvisor that we were good.

Loans have been primarily in his name due to him being easily w2 verified.

I got verified via one of those websites (verifyinvestor.com or similar).

Can you verify if the appraiser went on site or if they did ut remotely or BPO?

Verify that they have jobs (still) and that they have been consistently paying rent (on time).

I'd get a few other agents to triple check your comps and maybe even get an appraiser to verify your findings.

Are your verifying government ID? 

He had also not been informed by the selling agent and there was nothing on our contract to disclose them not being permitted.I realized I made a HUGE mistake in not verifying this information(noobie mistake) in further detail to ensure what was permitted or not.I also realize that there is a chance that the permits were pulled prior to 1999 and everything is okay here.

We did receive an email a few months ago from Aurora City Gov asking to verify that the Airbnb was in our primary residence, so it seems they are somewhat attempting to enforce that rule.