Don’t forget the two 8mm nuts that are installed from underneath the head.  One in front, just below the exhaust, and one in the rear, just below the intake.  These two nuts and studs need similar treatment.  Clean, well-oiled threads.

Tighten the cylinder head fasteners in four increments (70 inch-lbs, 140 inch-lbs, 210 inch-lbs, and 280 inch-lbs).  If you don’t have an inch-lb torque wrench, divide by 12 to convert to ft-lbs (6 ft-lbs, 12 ft-lbs, 18 ft-lbs, and 24 ft-lbs).  Tighten in a criss-cross pattern.
 
Between each increment, snug up the 8mm nuts underneath the head.  Their torque spec is 19 ft-lbs, but I haven’t figured out how to get a torque wrench on them.  Just snug them up after each sequence and on the final go round try to approximate 19 ft-lbs.

Thanks Mike.  I'm plowing ahead without addressing the cylinder wall issues.  Let's see what happens.

I'll wipe the anti-seize off the top side of the washers for what it's worth.

The 2 studs I had to reinstall hit bottom.  I didn't count turns.  I did leave myself a sharpie mark where they protruded when I removed them.  They are down in there to those marks.  Getting those studs out once was enough fun.

I used Restoseal 5 thread locker on the right rear.  It is PFTE based (teflon).  Personally, I don't think thread locker does a thing here.  It just gets squeezed out.  Trust the copper crush washer to do it's job.

I used straight 30 weight motor oil on the threads and nuts.  Threads were clean and the nuts turn like a hot knife through butter.

Yes, I know the stud torquing is a stretching application as opposed to a fastening exercise.  

Can you please share with me how you torque the main studs?  Pattern?  20nm first round, 30nm second round.  Or whatever practice you use?

Thanks again for all your help!!

Forging ahead.  Head studs torqued to spec.

I'm reinstalling the stock cam.  The following are photos of the index marks.

When I rotate the motor and get the mark lined up through the timing hole and the mark on the main gear is pointing downward towards the floor (6 o'clock position), the index marks are nice and level on the cam.  This is without tension being applied to the chain.

If I apply a little pressure to the chain (pretending to be the rear cam chain guide and tensioner), chain slack is removed.  The index marks on the cam tilt 2-3 degrees counterclockwise.  Please see photos if this description doesn't make sense.  I think I'm good here.  I don't think I can align it any better by moving the chain a tooth on the gear.

Am I in a slight 2-3 "advanced" timing here, or am I retarded?  (be nice!)

Position of cam index marks when turning the motor with no cam chain tensioner pressure on the chain (free riding chain).

The cam being off a degree or two is a sign of a worn cam chain. A new chain should have the marks right at 9 and 3 o’clock.

The "L" on the nut means nothing about timing.....that "L" moves around as you tighten/torque the nut.

The photo of the timing mark on the left side of the crank doesn't look entirely lined up - but that could just be a photo issue and not reality.

You should move the chain 1 tooth and see if the cam is better aligned.

Moved the chain over 1 tooth.  See next photo for chain slack on the front guide side with the marks in this position.