First, why tear the engine down at all? You can pull a jug or two if you're really concerned about the cam and take a gander inside, and easily dial the crank if need be...but with only 40 hrs I'd just bolt it on and fly. I'm just curious as to what you want to look at that you need a complete tear down on a 40SNEW engine that evidently didn't have a sudden stoppage or anything major to warrant it?
Second, $6k for a teardown and reassembly is too high. Most shops charge less than that for a full blown prop strike inspection...at least the shops I've dealt with.
Lastly, a small increase in HP is usually not too hard on these engines, but really large increases in HP will reduce the TBO as you are aware. One thing to keep in mind with all the cylinder work or if you increase compression is that in order to truly take advantage of it, you probably should also get a custom cam grind done, look at both the induction and exhaust systems, as well as fuel delivery and ignition systems. Anyway, be wary of HP claims by builders and shops. Without a dyno slip to confirm it, it's many times 'guesstimated' to a good extent.....I'd reduce anyones claims by a good margin unless they've got proof. Normally, the largest boosts in HP come from higher compressions and higher RPM's. Perhaps Rhonda or Alan or somebody can jump in here with their personal experience (they've forgotten more than I'll ever know), but in my limited experience HP claims are often like speed increase claims.....
As far as raw HP goes, the kings of that genre are in my opinion Barret, Lycon and Performance Engines (in no particular order). All three have good reputations among the highest and most extreme airplanes in the world.
Just my 2 cents as usual, but if it were me I'd bolt that thing on and go fly!
Cheers,
Stein