All in in with architects fees, Permits, HUD Consultant fees etc. his total rehab budget with a 15% emergency reserve became $398,372.

For those not familiar, this is where all of your permit/plans/housing trials and tribulations (lol) are housed for Baltimore City. 

You want to get the U&O before anything, then start pulling your permits.

Also: Time- The city permit process was really slow, which delayed the work at every step, ultimately months.

@Sejj JacksonYou have incorrect knowledge, here is what IRS says about loans from an IRA:"Loans are not permitted from IRAs or from IRA-based plans such as SEPs, SARSEPs and SIMPLE IRA plans.

They also had another addition that was permitted for the master. 

I know in my city permits are required for STRs and they are not transferable and many of the units that have been grandfathered in wouldn't meet the requirements on the new ordinance.  

Do i need to pay for a permit in order to rent it?

If its such a big issue, why dont you just pull your own permits as a homeowner and pickup a crew of subcontractors from the home depot or lowes parking lot.

Then to go Duval county site and search for the permits so you can find the GC that performed the work.