Put the new engine on a stand and strip it down to the block and head (remove the vacuum valve mounting plate from the top of the valve cover - the older EFI mounts them differently IIRC). Drain the oil. Check for any coolant in the old oil. Remove the oil pan. Check for any pieces of plastic (timing chain guide fragments) and thouroughly clean the pan (put the drain plug back in now). Turn the engine upside down. One at a time, remove the rod caps and check for wear. Good insurance would be to replace the bearings while you are there. After those, check all 5 of the main bearings. Go ahead and replace them, as well. These are the parts that usually get the most wear, and can lead to more serious damage if they fail. While the engine is upside down, Use a good, bright flashlight and do a good inspection of the cylinder walls. Rotate the crankshaft so that each piston is at TDC when you look at that cyl. Look for any vertical grooves (more than scoring) or galling in the bore. Go ahead and also replace the rear main seal (if this is close to the end of it's life, you will have to seperate the engine and trans later, and pull the clutch and flywheel to replace it then). If everything looks good, replace the oil pan gasket and oil pan (be sure to reinstall the oil pickup tube). Turn the engine back over, and remove the valve cover. Take a good look at the timing chain, sprockets, guides, and the timing chain cover on both sides (where the chain would rub if the guides broke). Check the valvetrain for any worn areas, broken parts and smooth function (rotate the crank) Check the rocker arm clearances. .08 for intake, .12 for exhaust. Put your valve cover back on. Now, take this long block and swap it in place of your existing block and head, and re-attach your EFI to it. Pay attention to the oil pressure sender. If the sender is different, you will need to swap your existing one to the new block. The "braces" that attach to the front of the transmission and to the bottom side of the block, attach differently from 2 to 4wd's. Use the braces for the 4wd, and everything will bolt up correctly.
If you do all of this, the replacement engine should give you the longest service life possible. Now, gather the 96 EFI system and list it in the for sale section, and you should get enough money to cover the cost of refurbishing your block.
