Transmission repairmen who regularly worked on COM's (from the '60's) are long since retired and today's shops haven't seen a Cruise-O-Matic in many years. They are good transmissions, but harder to find parts for. Same story with FE engines but on a smaller scale.
Now, 351W and AOD transmissions are very available at a much lower price. This combination may be found in many bone yards across the country.
351W's share many 5.0L parts including pistons, rings, water pumps, starters, etc., and had been original equipment in full size Fords, Thunderbirds, Mustangs, and trucks. (Ford sells more trucks than cars.) Many millions of Ford vehicles were powered by this setup.
The 351W/AOD swap makes better sense and is cheaper than converting transmissions. 351's came in different versions; EFI, carbureted, and 351W's also came in a hydraulic roller-cam version which is perfectly suited for use with modern motor oil.
The Ford Lightning engine (EFI 351W/roller) is one of my favorite choices because much of it is aluminum, bearing sizes are much larger than 5.0L, and performance parts are everywhere. Expect over 400-hp, naturally aspirated, with a decent roller cam. Lower rear end gear ratios like 4:10 or 3.90:1 are perfect when coupled with an Automatic Over Drive tranny. So, street performance and Interstate Expressway travel are both well suited to this setup.
The 351W sits lower and is lighter than the FE's. Kits are available to raise Squarebird motor mounts for a bolt-on conversion. A front-sump oil pan (like trucks use) must be used for Squarebird #2 crossmembers.
I suggest you keep your FE/COM off to the side with the driveshaft, in case you ever decide to go back to it. But if you ride your Squarebird a lot, bolt in a 351W and AOD trans. You may need to buy a driveshaft, but they are not expensive and many shops re-tube driveshafts, 'to length'. - Dave Dare