The way I do it is to use Aviation type Permatex or Gasket Sench on the block rails to install the cork gaskets then put the rubber end seals with only a tiny amount of silicon in each corner were they touch the cork rail gaskets then let it set until dry. Since your doing it in the car you might need to install some or all of the oil pan bolts loosely to hold the pan rail cork gaskets until they dry. You could then use a little bit of silicone on the cork gasket rails if you want (it isn’t really needed though) or use it only on the oil pan rails. Don't use any silicon on the rubber end seals except maybe at each corner sparely. Make sure the oil pan rails are nice and straight and don't over torque the oil pan bolts or it will damage the gaskets. Good luck 
Looking for an update on your progress. Did you ever get the old "Rusty Wagon" back on road and everthing working Ok?