Does the same procedures apply to wholesaling duplexes, triplexes, or multi family units as when doing single family properties?

To me this is a case for a real estate attorney to handle for you even the due diligence on it and let him get as much information , detail or procedures for you.

It appears so; here's a quote from this link:"When making an offer on a short sale the proper procedure is you write into the purchase agreement that your deposit check is to remain UNCASHED and held either by the buyers agent or the escrow until the short sale lender approves the short sale.

Get a title company and title insurance, kindof standard operating procedure and best practice...

But I was curious if someone might walk me through the procedure they've used when a tenant moves out, as far as clean-up and prep for the next move-in?

People tend to be less formal with roommate situations, but you should be more formal with your procedures/agreements. 

Just a quick update I just got email from title company they told they just got off the phone with listing agent and we are not getting anywhere with this guy, (not sure of conversation ) they faxed  over all closing procedures also faxed them to my buyers agent and was told to proceed with closing I'm don't know how this is going to help with DYE Test , I'm sure listing agent is not going to give key code for property.

My wife works HR for a property management company so we followed procedures to a tee and had possesion within 5 weeks for about $65 total cost along with a few hours off from my full time job.

If the city followed all the proper procedures in changing the zoning you may well be out of luck. 

Your attorney will know what the law and local rules of court procedures require for construction AND actual notice.