Installing Engine

Please refer to the Engine Swapping section as well!
Precautions

I've found it helpful to support the front of the car by jackstands when you go to put the motor in, so that the weight of the motor doesn't cause the front of the car to drop down once installed, messing up the alignment of the tranny on its support, etc. This helped me to be able to drop my motor in singlehandedly, whereas I usually had to fight to get the engine to mate with the tranny, engage the torque converter, and land on the motor mounts, even with another person helping.

Lubrication, or the lack thereof, affects torque wrench readings. Dry readings with vary, while lubed reading are reproducable. The shop manual usually specifies whether or not to oil the fasteners. If you don't have a shop manual, get one. One of the best investments you'll make.

Scribe marks, paint, or locating holes notwithstanding, the hood will not be perfectly aligned when you reattach it. DO NOT blindly slam the hood the first time. Check for alignment carefully and adjust as required.

In addition, having more than one of the same car makes it very easy to figure out where something goes - you have a full-scale model.

Get all new hoses; this allows you to simply cut the old ones off, possibly saving your heater core (which might spring a leak from all the twisting and turning to get the old hose off; it's worth the $5 in hose).
Consider getting the correct hoses & checking each out before you cut the old ones. A good way to cut the hoses is to slit them at the connection so that they can be spread open & off. Cutting them around their circumference still causes you to put a lot of pressure on brittle old metal parts that don't need this type treatment. Reinstallation can be made easier by coating the inside of the hoses w/Vasoline at the contact places. It allows easy later removal too - even years later.
Always a must with a new engine. If you spend $2000 on motor, and many hours or weeks making a pro-show engine compartment, do you really want to risk running an old hose that might easily pop due to the increased heat load of a new engine?

Also plan on buying new fuel, oil, and water pumps, and all filters, new oil, antifreeze, and trans fluid and filter/pan gasket.
Also, there is no sense in running the old, baked tranny fluid through a new convertor. While changing tranny fluid, make sure to flush out the cooler lines and cooler. They'll hopefully clean out the cooler at the radiator shop. If you're due for a new engine, odds are the tranny fluid needs it, too, cuz probably over 95% of trannies don't get their oil changed every 20000 miles like they are supposed to.

While the engine is out, replace all expendable/consumable parts, such as hoses, thermostat, distributor cap and plug wires, plugs (of course), filters, belts, rubber motor mounts, starter drive and brushes (didn't think of that one, did you), exhaust doughnuts (if so equipped), etc. This rapidly gets into serious mightaswells.

Put the heat shield and braces on the starter (instead of throwing them away, like usually happens when installing on the car)

As you slowly lower the new/rebuilt engine back into your shiny new engine compartment, you will be thanking me profusely that I talked you into getting that engine tilter. The option when the engine is at the wrong angle (not if, when), is to either pull it completely back out and reposition the chain, or to set it down on your freshly-painted crossmember and watch in horror as it slowly tilts towards the inner fender panel.

Getting Down to Business

All bolts being reused should be thoroughly cleaned and lubricated for installation. Pay particular attention to the six bellhousing to block bolts (voice of experience on). These bolts must be properly torqued (he said, examining knuckles slashed from sharp points protruding from firewall) and should likely be installed with Locktite. Should they loosen (which happened twice on my first 442), the flexplate will really flex, leading to rapid fatigue failure and cracking (since the crank and transmission centerlines will not be parallel).

When reinstalling, put a dab of grease on the pilot area of the torque convertor. I'd never seen it happen, but heard of it in college. Under heavy stall conditions, the torque convertor actually balloons, and expands into the center of the flexplate. This is alleged to be a normal condition. A dab of chassis lube on the end of the convertor will prevent any binding during this occurrence. We hope.

Before reinstalling, make sure the torque converter hasn't moved forward (do you get the sense that there are some lessons learned here?). If so, push it back onto the input shaft while turning (there are several concentric splines which must line up).

[ Thanks to Bob Barry, Scott Mullen, Joe Padavano, Charley Buehner, Bob Barry, Bill Culp, Glenn for this information ]