Problem with putting anything else in then Mercury power is that they are hard to sell, you get hit over the head.
I had a 39 Nortech that I put Zuls in it and it was hard to sell, I traded it in for my MTI. and made sure it had Mercury power in it. I know what the 850/1075 Mercury engines cost to rebuild, but do not know what the 1100/1350 Mercury rebuild cost is or if they are really getting the hours out of those engines like they said they would.

With the differance in price of non Merc motors in the boat you should be able to sell the boat a lot cheaper then if it had Mercs.

What about a pair of 700's that are turned up a bit.

I know Merc 700's are strong running motors with little issues and with the type of boat you are building you have a base idea of the speeds you will run.

Just as a tidbit of info....Flight Club owned the "Tainted Lady" 48 V Skater and removed the big Sterlings and installed Merc 700's with Stage 3 Whipple kits. Boat was well over 100Mph as documented in the Skaterfest threads.

Good tradeoff from mega HP for reliability while keeping the Speedo in the upper range.

Merc 1100/1350 have a unique following - there are those that are totally against due to reliabilty/ warrantee issues and others that will not build a boat w/o them for the principal reason of the ease of selling a Merc Boat.. which seems to carry weight when selling a boat under 2-3 years old.

Big power... Go Merc!!!!
May be more expensive up front but the reliability and resale value make it well worth it!

What is the real resale value/difficulty difference in a top end boat resale Merc Vs. Custom Engine builder. Is there a real number?

If you save $100K up front, and you take that same number off the resale, it sounds like a win/win all around. I think the whole "Merc resale" applies more to the mainsteam go fast boats than the super high end. Mainstream of course being a relative term.

Case in point:

My friend sold Speed Racer with Ron Potter engines in it not that long ago and got pretty much what he wanted for it. He priced it right and waited for the right time/buyer. It didn't seem to effect his resale. He also bought it without engines which is also not uncommon with the big boys.

That said, I have "575 Mercs" in my boat that Ron Potter rebuilt to 700's but we left them Merc Blue with the Merc valve covers on them (the air cleaners proudly wear Ron Potter on them). Why? Because the market for a boat like mine is accessible to a larger market of buyers (some not as into the whole go fast realm as others). It is a more competitive market with a lot more boats and with buyers on a tighter budget than that looking for a top end cat. These buyers are very familiar with the name Mercury and in reality it is really just a preconceived notion of reliability.

Yes, Mercury Racing does have a big edge in technology and turbos seem to be working well so far.
But, we all know that anything can happen at any given time no matter who's name is on the engine.
Personally I like knowing that Ron carefully hand built my motor and personally puts his name on it.

Your definately in a tough spot with a new boat. I think it is pretty well known that they are having some problems with the 1350's, and they are not going to be cheap to fix after warranty. I agree in the past Merc 1075's were the way to go, especially for resale. HOwever I know of several boats for sale mostly because they have the 1350's and the owners are worried about the next $100K hickup. So the resale down the road may not be as good for the 1350's as it was for the 1075/1200's. As far as rebuilds on 1350's, I would figure the cost of new 1350's bobtails less the core value, which they have posted and is scarely low. That would give you a worst case price. I think at Sema I saw estimated price at $65K, and I believe the core has been stated at 3-8K. So that would leave rebuild/exchange at $57-63K per side. This might be slightly on the high side or not, but it will get you a safe estimate so your not shocked when it comes.
Then the decision becomes can you get that much more resale over a good EFI Precision Marine or Teague combination.
I know its easier to spend someone elses $$, but if I planned to keep it for any length of time I would not go the Merc route. As I don't think they build any better motor, their rebuild is insane and I really question what the reale is going to be on boats with this rebuild price looming.

At that price point why would anyone trade in their core instead of selling on the open market for way more than the amount that Merc is willing to give for a core??? The problem with these 1350's is that there is not a secondary market yet, once a bunch of them are out of warranty and second hand people start having parts for them, the prices will come down dramatically.

At $55,000 to $60,000 aside for a rebuild is crazy, but I think it's a high number because not many engine builder are not rebuilding the new Mercury engines yet. Give it sometime and those prices should come down.
Makes me think the 850's and 1075's engines will stay in good demand.

OHC multi valve engines allot more moving parts than a pushrod engine .