Wow, no responses. I wonder why?
Anyway, IMO, just clean up the surfaces to take the liner measurement. Be sure to check on both sides, they may not be the same.
I have no suggestion for head gasket or coating. I've had a lot of trouble in the past, tried several different gaskets and coatings with pretty much the same results. Using a regular copper clad composite gasket combined with soldering a "fire ring" to it is what works for me. It's my belief that the liner protrusion being low on one side is my problem (I never had problems with several previous engines using just a cheap gasket from JCW and no coating); the fire ring is a workaround for that. But given how well it has worked out, I may do that next time as well, even with the correct protrusion.
I don't know if it's "best", but what I do is 60 ftlb the first time, then 80, 90 and 102. I know the book says "100-105", but torque wrenches are never perfectly accurate (when is the last time you had yours calibrated?) so I shoot for a reading in the middle of the given range. ISOA ran an article some years ago where they compared several torque wrenches against a "digital" torque sensor and found that both the overall accuracy and the deviation from one reading to the next were fairly large. For example, in 5 trials, the Snap-on dial type torque wrench gave actual values (as indicated by the torque sensor) from 49.9 all the way up to 53 ftlb for a wrench reading of 50.
Workshop manual says to retorque after 500 miles, not just head nuts but manifolds and so on. But it certainly will not hurt to retorque multiple times, both sooner and later. I generally check after the first heat cycle as well. Best practice IMO is to keep track of nut position, and keep retorquing from time to time until they always stop at the same position. My front and rear manifold nuts (the ones without the bridge piece) used to always go some more until I added some heavy flat washers (aka "setup" washers) under the lock washers.
Note that when taking a torque reading, it is important that the nut still be moving when taking the reading. If it stops moving, it will take extra torque to get it moving again (an effect known as "stiction" for static friction). For that reason, when retorquing head nuts, I always loosen the nut a bit first, so I can take the new reading with it moving. Doesn't need to be very far, just a fraction of a turn will do fine. But I don't bother with that (or even using a torque wrench) when doing manifold nuts.
Make sure your head nut washers are in good condition. The factory apparently used relatively soft washers, and they tend to crush in service until sometimes they won't even slide easily over the threads. IMO replacements should be at least Grade 5; the ones I use are harder than that. Of course all the lock washers should be replaced with new as well.
If you are reusing studs, clean the threads with just solvent and a rag, then try spinning a new nut down the threads. If it binds partway down, discard that stud. Chasing threads is fine in other places, but not IMO for high stress applications like head nuts, rod bolts or flywheel bolts.
Hi Guest!
Hey - did you know if you click on the title of a thread it will take you to the first unread post since you last visited that thread?
but were afraid to ask: 
STOP!! Never post your email address in open forums. Bots can "harvest" your email! If you must share your email use a Private Message or use the 
smilie in place of the real @
Pretty Please - add it to our Events forum(s) and add to the calendar! >> 
