I just recently went through an engine replacement on my Land Cruiser. I bought it with a blown head gasket and I knew it would need a new engine when I got the truck. It was relatively cheap and even with the engine replaced the money I would have in the truck would be well below any book values for the truck. I had a local mechanic that my stepdad uses for all his stuff. He's a used car whole-seller so he's always buying stuff that needs work or whatever. The difficult part for my truck was sourcing an engine. Since it's a 2007 the field of candidates was pretty small. My dilemma was deciding on going with a remanufactured engine vs a used engine with as low miles as I could find. Unfortunately the used engine avenue also opens up a ton of unknowns. How was it treated, why was it pulled, how long has it been pulled, where and how has it been stored, and so on. Then came the cost. Unfortunately I no longer have the time to do an engine swap myself so I was going to have to come to terms with having someone do the work for me. The truck sat for over a month because no one had an engine for it. None of the rebuilders had an engine and the few used ones we found were questionable at best. In the end one of the rebuilders the mechanic uses often had an engine come available. I guess one of the pluses was the engine was newly remanufactured and had not been sitting somewhere collecting dust.
When it was all said and done the remanufactured engine plus install and replacement of all the "while we are in there" components such as pulleys, fan clutch, heater tees, starter contacts, hoses, belts, and I'm sure I'm missing other things, was within a couple hundred dollars of using a used engine. The remanufactured engine came with a 4 year 100k mile parts and labor warranty. Something I wasn't going to get with a used engine. I've only put about 1000 miles on the truck since I've had it out of the shop but there are no weird noises, engine codes, leaks, or any other abnormalities.
I wouldn't be worried about using a remanufactured engine over a used one. Though different years may have better luck sourcing a good used engine. I would definitely get a documented warranty on the work performed.