Reply to "Is there a known "Engine Out Check List"..."

1. Replace cooling tubes
Good time to replace the stock steel cooling tubes under the car with stainless - only time you can remove and replace the long one is with the engine out, unless you get under there with a sawzall and replace it with shorter lengths.

2. Repair rust between tank and fender
Also, while the gas tank is out to be cleaned you should check the inside of the quarter panel between the tank and the fender for rust/corrosion. Dirt and debris is collected there, then it holds moisture and begins to rot the panel from the inside out, so fix anything you find there now too.

3. Install removable lower cross-member
It's a good time to remove the welded in lower cross-member and replace it with either a removable cross-member or a lower chassis stiffening kit. That way you can remove your oil pan while the engine is in the car if you ever need to service/inspect the bottom end. Removing the cross-member can be done while the engine is in the car, but it's a lot easier to do when the engine is out.

4. Strip and refinish your engine compartment
Remove all that factory undercoating that attracts and holds dust and dirt and either repaint the engine compartment or coat it with a durable bedliner material to maintain a stock appearance (but better looking) that cleans up easier. Before applying the new finish to the engine compartment is also a good time to weld up those holes back there that let water down into the frame rails.

5. Coat your headers and exhaust system
Any of the quality coatings will do - JetHot, Ceramacoat, etc.

If I think of more, I'll add to the list.