Docking the engine to the transmission was uneventful but tedious and time consuming. It was more difficult than for my 4.0L SOHC V6. The 4.6L access hole for the torque converter nuts is smaller than the 4.0L starter motor hole. Also, once the rear of the flexplate is aft of the face of the transmission housing the studs on the torque converter adapter are no longer visible. My torque converter was fully aft on the transmission shaft for the engine docking. The process would be easier if the torque converter adapter studs were forward of the face of the transmission housing to simplify aligning the studs with the flexplate holes. My process is as follows:
1. Rotate the crankshaft with the harmonic balancer retaining nut until one of the holes in the flexplate that mounts to the torque converter adapter stud is centered in the access hole in the block.
2. Rotate the torque converter adapter until one of the mounting studs will be centered in the access hole in the block.
3. Position the block in front of the transmission housing and adjust the forward to aft tilt so the face of the flexplate is parallel to the face of the transmission housing.
4. Position the block using the crane and leveler so the two block to transmission housing guide bushings are aligned with the transmission housing.
5. Align the transmission adapter stud with the flexplate hole. If the stud is above the flexplate hole place your finger thru the large hole above the small hole (red arrow in photo below) and push the stud downward.
If the stud is below the small hole, position something flat and thin between the flexplate face and the transmission housing face to push the stud upward. I used a small jeweler's screwdriver to keep the stud centered in the hole.
6. Alternately from side to side use transmission housing to block bolts to pull the guide bushings into the transmission housing. This should only require a few lb-ft of torque. More than that indicates something is binding. The studs may not be aligned correctly or the flexplate may not be parallel to the transmission housing. Continue tightening the bolts until the block face is seated against the transmission housing.
7. Start a nut on the torque converter adapter stud. I don't like the locknuts Ford uses. I prefer a thicker nut with less rounded outside face. So I purchased four M10-1.0 nuts from AutoZone. I will use medium strength thread lock when I torque the nuts to specification. Since the torque converter was fully recessed in the transmission housing and the flexplate is thicker than stock only one or two threads of the stud were exposed on the flexplate. I found that the threads on the nut were closer to the face on one side than the other. So I was able to start the nut with my hand and carefully tightened the nut pulling the adapter forward.
8. Rotate the crankshaft 90 degrees clockwise and start another nut. Repeat until all nuts are started.
9. Tighten a nut until snug and then rotate crankshaft 90 degrees clockwise while checking for any binding. Repeat until all nuts are snug.
10. Torque a nut to specification if using Ford locknuts or remove nut, add thread lock to nut and then torque to specification. Repeat until all nuts are torqued to specification.
11. Insert transmission to block bolt and torque to specification. Repeat until all bolts are torqued to specification.