I see recommendations for Kohler Commands and Vanguards but not Honda. The folks at repowerspecialists.com who sell all makes at similar margins recommend the Honda GX690 when looking for reliability and longevity. According to them the Honda is made to operate at higher temps and in hot climates it is tough to keep the Command or Vanguard cool enough. I asked about Honda's reputation of not being what they used to be. The response was that it's true for the consumer line of Hondas, but the commercial Hondas are still the best thing out there in a gas engine. They pointed out the advantage of the Command's hydraulic lifters but believed love for the Kohlers was based on having other Kohlers in the fleet and/or keeping things made in the USA more than reliability and longevity. So since the OP was asking for engine recommendations, I was wondering about the "whys" behind your recommendations and wondered if any Honda Guys could chime in with good or bad experiences.
Coworker of mine has a Honda in his 2082. It ran hot out of the box. I've also read that about Honda conversions from the JD guys. Good thing it's made to operate at higher temps
Not sure if this was specific to my coworker's engine, but the grass screen was attached to the flywheel shroud and not the flywheel, so it clogged with grass easily. He added an extra fan to the front end of the driveshaft to stir things up a bit and keep the grass from sticking. The design of the air cleaner assembly (not sure if this is still true on the most current version of those engines) draws in hot air in a Cub Cadet type installation. Oil cooler design and placement is not effective. I think he also said the pipe thread fitting for oil pressure sender is BSP instead of NPT. 2-barrel carb is finicky, difficult to clean, and parts are expensive. He finally got it to stay cool and run well, and now likes it, but it was absolutely not a drop-in installation to get it there.
I put exhaust gas temp (EGT) probes on the Command on my 1872 after my conversion, modified a spare carb to be adjustable, and after some experimentation, found that the factory mixture setting is just barely richer than the mixture that corresponds to peak EGT. I rejetted the carb and got the EGT to decrease 100 degrees. This should do wonders for performance and longevity. I honestly doubt a Vanguard or Honda would be any different, as all have to comply with the same emissions regs that drove the manufacturers to this stupidly lean mixture.
I added an oil cooler (bolt on from a larger Command, and much better design than the Honda one, IMO) and a duct to get the air from it moving out the front, and it runs nice and cool. It will hold 32 psi oil pressure while mowing in 95-degree weather.
The Command engine has Japanese roots if I recall, so the "made in USA over reliability" just sounds like some competitor's sales smoke and mirrors to me.
Any of these modern V-twins will require better sealing of the firewall in an enclosed installation so that they only draw in fresh, cool air for induction and cooling. I think most people have overheating issues with repowers because they don't address this issue.