Before proceeding further, I'll suggest that the oil pan be put in place with everything clean but without the gasket.  Then take a feeler gauge and see exactly where the distortions are between the pan and the retainer.  Once this is known, then you can make a suitable correction.
  
If that fails, I’ll suggest a thin bead of RTV and then the gasket on top of that but only in the retainer area.  You didn't mention the brand or composition of the oil pan gasket which can be a player.  I can see where cork would be a problem in your case.

Using RTV by itself without an oil pan gasket would be a mess and very difficult to clean the next time the pan would need to be pulled.  I've pulled down other brands of engines where this was done and they were still leakers at the oil pan rail which means RTV is not a cure all.   If the pan is only leaking at the rear seal retainer area, then that would be the only area I would consider putting a thin layer of RTV.  It’s important that the RTV be allowed to ‘skin over’ before actually placing the gasket on top of it.  In your case, you may need RTV on both sides of the gasket at the rear seal retainer area depending upon if the pan or the retainer or both is the problem.

Lorena, Texas (South of Waco)

This maybe revelent to my problem but I don't think so. I have a 312 crank installed with the slinger removed. I find not a sign of oil leakage at the crank flange so really hate to disturb that seal. I placed the pan on the block and I need to get it to contact better especially at the rear. The gaskets I have used are all cork,2 were Fel-Pro OS10701 C-1, 1 was from a gasket set, Pro Torque KS32120. I was careful to not over tighten the gaskets. I believe that Victor also has a pan gasket and I will get that one which I may install. Has anyone used the Victor? Earlier it was mentioned about crankcase venting. All looks good there if you will take a look at a video post of the engine running.

56 VIC  Gene Stoehr Sr.

I have both pan gaskets. The Victor is thicker, .015, than the Felpro. Also the cork material seems to be denser. My question is where do I start the RTV sealer? Do I use a little bit of the RTV with Permatex on the back edge of the pan or stop the Permatex at a given point and start the RTV? I think the Victor gasket will take a little more torque than the Felpro.

56 VIC  Gene Stoehr Sr.

Permatex is a brand which produces many products, including RTV.  When you say Permatex, which product are you talking about?


Lawrenceville, GA

Aviation Form-A-Gasket sealant liquid.

56 VIC  Gene Stoehr Sr.

I’ve had no issues with the rear seal crankshaft slinger being removed from the crankshafts.  When installing some of those 292 sized rear main seal cranks in the early 272/292 blocks, the slinger had to be removed from the crankshaft simply due to the early blocks not having the groove in the block to accommodate that crankshaft slinger.  Where I’ve seen a majority of oil leaks at the back of the Y is with the side seals on the rear seal retainer.  A dollop of RTV in the hole before installing the side seals seems to take care of this area in most cases.  In rare cases, I’ve found the rear seal retainer either cracked or warped at which point the retainer is simply replaced with a usable unit.
 
You don’t mention how you’re tightening the oil pan bolts.  Using a torque wrench at this spot can get you in trouble so hand tightening is recommended and then only tightening the bolts just enough that you see only a slight deformation in the gasket as it’s being squeezed in place.
 
In your case, I’ll suggest getting away from the cork and into something more substantial.  I use the Best Gasket oil pan gaskets which is a ‘black’ dense fibrous material for want of a better description.  These oil pan gaskets simply get coated with white grease when installing them and are leak free.  Due diligence is taken before hand to insure that the timing cover and rear seal retainer are flush with the pan rail.  The oil pans are also dry fitted to the block or a flat surface to insure that the sealing rail is flat.  The oil pan bolt holes are reverse peened to get the oil pans’ sealing surface flat where necessary.
 
I have managed to reuse the Best Gasket oil pan gaskets when needing to remove the oil pan for various reasons.  The 2016 EMC Y used one of these and had to be torn down at the competition.  That particular used oil pan gasket has been reinstalled back on the engine twice since then and is still leak free without using any sealer.
 
I’ve used oil pan gaskets using a similar ‘black’ material that are available by FelPro for the Ford FE engines; these gaskets are available as an alternative to the cork oil pan gaskets also available by FelPro for the same engines.  FelPro calls these gaskets rubber coated fiber gaskets.  I’m not aware offhand if this material is also available by FelPro for the Ford Y engines but any retailer that handles Fel Pro should be able to look that up for you.

Lorena, Texas (South of Waco)

Thanks Ted, I will check out the Best Gasket before I install the pan. I don't have any leaks at the crank seal or the side rails. I was careful to hand tighten the pan bolts on every pan gasket I installed per your method. I will have the pan with good contact all around before installation.


56 VIC  Gene Stoehr Sr.

Ted, This white grease? Is it white lithium grease? I looked for just white grease at NAPA didn't see anything but WLGrease.


56 VIC  Gene Stoehr Sr.

Yes.  It would be white lithium grease.

Lorena, Texas (South of Waco)

Thanks Ted. I be putting that pan back on next week. I will post how the Best Gasket does.


56 VIC  Gene Stoehr Sr.