With the heads now prepped and ready to go we turn our attention towards completing the longblock. A longblock is what you call an engine that is complete from valve cover to valve cover and has the flywheel attached, yet no peripherals, i.e. intake, exhaust and so on.
The first order of business is getting the pistons ready. Essentially this means setting the ring gaps, checking their side clearance and checking piston to cylinder clearance. You want to use a piston ring tool to remove all the rings, but keep them in organized sets with regard to what piston and cylinder they came from. It doesn't matter that much now, but it will once you've checked and adjusted the gaps as needed. The general rule of thumb for ring gaps is that you should have about .004" for every inch of bore. So for a stock 85.5mm P/C set this would give about .0135" gap which corresponds to the factory tolerance of .012"-.018", oil scraper rings can be a thou or two tighter. You can use this same formula to determine what gap you should be running on larger piston and cylinder sets as well. Ring side clearance should be right around .003" for the top ring and .002" for the bottom ring with a wear limit of roughly .001".
Finally piston to cylinder clearance is best checked by mic'ing the piston and using a bore gauge on the cylinder. Clearance here should be from .0016" -.0023" for a stock bore engine. If you're too tight, you can have your machine shop hone your cylinders to spec.
With the rings setup and the pistons ready to go, you
can now begin attaching them to the engine. Do just one at a time
and go slowly so you don't scratch them up on the head studs. Put
a piston in place and slide it's wrist pin in with the aide of some assembly
lube and then secure with circlips. Then use a ring compressor to
hold the rings in place as you slide the cylinder over the piston while
carefully guiding it into the case bore. I like to use the same
Permatex Form-A-Gasket sealer on the cylinder bases that I used on the
case halves. It has always kept leaks at bay and been very easy
to cleanup on future rebuilds. If cylinder base shims are to be
used, put sealer on both sides and slide them over the cylinder skirts
before installing the cylinders.
Loosely slide a head into place until there's just enough room to still install the pushrod tubes. It can be helpful to have someone holding them in place while you work the head. I usually set the head on just enough that I can squeeze the tubes into place by myself, but be careful, the ends are quite sharp. When each head is in place you can begin torquing the heads down according to the sequence found in any VW manual (Bentley, Haynes, etc), but alternate between heads to keep the applied torque from one side of the case to the other as equal as possible. I also like to add a few middle steps and go from 7 ft*lbs to 15 ft*lbs, then 20 ft*lbs, and then a final 25 ft*lbs for 10mm studs. If you are using 8mm studs, then just go from 15 ft*lbs to the final 18 ft*lbs.
Now that the heads are on, you can install your pushrods and rocker assemblies. Rocker arm geometry is easier to set before the heads are installed provided you know your actual lift numbers. The procedure for setting geometry can be found here. Be sure to use a dab of assembly lube on the tips of the pushrods before installing. You will also want to assure there is plenty of oil/lube on the rocker assemblies themselves too, this is the last part of the engine to get oil when the engine is started up, so make sure there's plenty now. Install the valve covers now to keep debris from getting into the heads.
With the heads on there is only two things left to do,
set the endplay and install the flywheel. Be sure the o-ring is
installed in the flywheel and you’ve smeared a little assembly lube
or engine oil on it. Also be sure to smear a little oil on the flywheel
shims as well. The easiest way I';ve found to set endplay is to
pick any two shims, install them, then torque down the flywheel to at
least 100 ft*lbs and be sure to lightly oil the threads to prevent galling.
With the two shims in place, take an endplay reading with your dial indicator.
Then simply subtract the number you're aiming for from what you measured
and then find a shim that size. If that size is unavailable, then
change one of the two shims for another size that will help bring the
measurement of the third shim into the range of what's available to you.
Spec is .0027" -.005". For a stock engine, I always aim
for .004", for a more performance minded engine, I go for .005"-.006".
Even though it is possible to finish up the engine and do the break-in run on the same day this step is completed, I recommend letting it sit for a full day before doing so. This allows time for the loctite on the gland nut to fully cure. The last thing you want is to have your flywheel come loose on you, it usually means you're doing another rebuild.