Hi John,
How and when to apply sealants, and what to use can sometimes be a topic of many opinions. But I think everyone would agree that you must put sealant between the washers and the heads on the four cylinder studs that sit under the valve covers. I use Permatex Aviation Form-A-Gasket (#80019). It's probably available from any VW aftermarket parts supply source.
Regarding the push rod tubes: They "say" the silicone / rubber cone washers that come with the tubes don't need sealant. You probably already distrust that idea, which is what is leading you to replace the push rod tubes in the first place. I finally gave up on that idea myself and use liberal application of Permatex Ultra Copper High Temp Silicone (#101BR)to seal the inside and outside diameter of the cone washers.
I also use the Ultra Copper to seal the cylinders to the case, especially in between and around any shim spacers that are quite possibly between your cylinders and the case. Since you have removed the heads, you might want to think about the seal between the cylinders and the case. If a hard sealant was used (like Form-A-Gasket) at the time of build, then it is possible the sealant might have broken loose or "cracked" if you knocked the cylinders during all of your playing around. Right now would be an easy time to slide the cylinders up from the case, clean the surfaces of the mating pieces and reseal it all together again.
A word about silicone rubber sealants. Some experts absolutely hate them. Some think they are the greatest thing since . . . . silicone. I think all would agree that if you do use them to always be mindfull that if only a small fleck of silicone rubber can break loose inside the engine and eventually wind up plugging an oil hole it would be a bad thing. So make sure that you apply silicone only in instances where if the parts are pinched together that blobs of silicone never ooze to the inside of the engine case.
If you are replacing the push rod tubes, I suggest replacing them with the spring loaded anodized aluminum kind instead of the VW stock crush bellows kind. This suggestion will also have expert differences of opinion. But I like the idea of the spring loaded push rod tubes for the very reason of your primary concern: Leaking. If you do get a leak with the spring loaded kind, you can remove the push rod tube for servicing without removing the head (an advantage I think you would have already come to appreciate).
Anyhow, those are some "brief" thoughts.
Mark
