Deferred maintenance is often a simple/cheap (relatively) fix, but neglect can be the cause of major systems failures or issues, which can destroy your returns, so be sure to have a very thorough inspection.

Does anyone else have this issue?

Id say the issue here is a little more shady than your typical transfer of a property into an LLC. 

Shouldn't have any issues under Treas Reg §1.163-8T(e)(1) above."

Normally you should call the police, but it may not be worth it and will inflate an issue that most likly is going to go away by itself once you have rented your property.  

I will also create an upfront operating account fund to cover any unexpected issues that occur before I build an adequately sized reserves account from the ongoing savings. 

As far as compliance, as long as you have the note forwarded with a servicer which is licensed in the state where the note was originated, then is obligated to keep everything in compliance and should advise you if there are any compliance issues. 

This is only an issue if you work with larger banks and they sell off the debt to Fannie / Freddie.

I was planning on doing BRRRR but there is a foundation issue that makes it unable to obtain financing.It is a 1200 sq ft ranch on footing with difficult to access crawlspace built in 1952.

If unit access is not granted with reasonable notice, issue a Notice of Material Breach.