I've seen it a few occasions the title company sent the EMD back to the buyer because it sat with them 2 years.

For those of us living in Wisconsin we use Wisconsin Legal Blanks. 

Texas even provides a pdf fill in the blanks form.   

We did have confusion regarding where the physical, blank checks would be sent to, but it all worked out.

If so does this mean I would pay the impact fees on 2 separate occasions when each pair of building permits are pulled (even though all 4 units are on one parcel) or do I have to pay for all 4 at once? 

It should include a few exhibits attached like a scope of work, a blank change order form, a final layout illustration, and a lien waiver (for the final payout) that they sign before starting.

It was a pizza shop and now is a blank slate. 

Here, once you have an account and a bit of lending experience, you can access the online, fill-in-the-blank templates to create your own set of documents. 

Except I'm a lot older now, and have a decent amount of cash with a blank slate.

In fact, by doing so, you're breaking the lease terms by blankly refunding security deposits.