But they may fear what may happen after they take possession and we aren't there to provide solutions.

If you bought a good duplex/location, you could/should have specified that the property was vacant when you took possession and verified same. 

Other issues aside, once you take possession of the funds, it's taxable.

I would have tried to contact the person whom had possession of the place before me to see about obtaining door keys, garage openers, etc. rather than showing up with my power tools trying to drill through the front door.

During this time you will have the right to forcibly remove the tenant and their possessions out of the property.

You are much farther ahead to take possession with vacancy.

At same time as eviction form I also file to schedule the hearing to gain judgement for possession, this takes 5 minutes and costs me $50.

The bank took possession in January this year.

I was thinking about changing the 'date of possession' on the purchase agreement but I'm not sure and don't want to make a small problem bigger by fudging numbers.

My first advice would be to walk away if you can't have possession of the house on the day of closing.If this is your dream house and you're determined to buy it and willing to put up with this BS, then the first step is to be absolutely certain the lender who's approving the short sale is fully aware the seller is staying.