One consideration in selecting the engine that was passed on to me by a very experienced builder was the resale value. Anything other than a zero time engine in new airframe will reduce the resale value and reduce the number of buyers who will consider your aircraft. Even a 1000 hour airframe is less valuable if the engine has more than the 1000 hours on the airframe.
While I am not planning on selling my RV-10 anytime soon, the time will come some day. So with the combination of the safety considerations expressed above, plus resale value impacts, and the potential increased time/effort that would be required to install a different engine than the IO-540 that the RV-10 is designed around, I made the decision to order the engine & prop as a package from Van's.
One other suggestion. Don't purchase the engine until you are about ready to install it. The warranty clock starts when the engine ships to you, and while Lycoming did a great job of preserving my engine, I would like to have warranty still in effect when I do my first start. (Just realize that delivery is several months after you place the order, so take that into account when deciding when to place your order.)
Best of luck with your build.
This was my thinking when I bought mine about eight years ago. That isn't my thinking today.
I went with the Van's deal. Lycoming just started shutting down the kit pipeline to builders. I was a couple months late. I didn't want an overhauled engine for all the reasons you mentioned.
I had a variety of issues, like the fuel pump quit of the first flight, and quite a few stupid questions since I never had to maintain an engine before. Van's doesn't deal with FWF issues. Lycoming was hit or miss depending on who you got on the phone.
I was fortunate to meet Rhonda and Allen from Barrett Precision Engines before I started my build. Both Rhonda and Allen have been supporters of the RV-10 community for years. Both have been helpful in my engine education and cordially answered my questions, even though I didn't buy my engine through them.
When I made my purchase, but a Thunderbolt through Van's wasn't an option, but it is now. That gives you a little flexibility in your configuration.
I don't trust Wentworth, although I know several people that have got great deals from them. You have to know exactly what you want and don't listen to their sales hype. They were pushing a 540 out of a helicopter that isn't anywhere near the same as a D4A5. Allen Barrett and a tech in the Lycoming booth at OSH educated me and prevented me from making that mistake.
If I was doing it all over again, I would purchase from Barrett. Rhonda and Allen are good people and take care of their customers. Sometimes they can get overwhelmed with new business, like right after OSH. That just means that it will take a bit longer, but they'll tell that up front. They are also great at letting people stop in and watch their build. Martin Filiatrault recently posted his experiences with Allen on his blog. I have another friend that is having some work done and I believe he is going to visit the shop next week.
I now firmly believe having Barrett find a case and overhauling yields a better solution that buying the Van's engine off the Lycoming factory line. I think it's easy to translate better, personal support as a better value proposition than a zero time engine.