I have a 427 ci in my 69, The air cleaner
assembly is new,and when I close the hood,
the rubber seal fits to tight, and it raises
the hood up,The hood is adjusted correctly,
and I do have a 3/8" insulated carb spacer
gasket on,My question is, is there a process
that I can use to mold that rubber seal to
fit better, so the hood closes better?
Also I am looking for two 427 hood emblems.
Any help with either,would be greatly
appreciated.

I don't know what combination you have, but the seal should fit when combined with a high rise intake, stock motor mounts, and stock air cleaner. You should not have an extension between the air cleaner and the flange ring for the seal.
If all that checks out. yYou might be OK if you just remove the carb spacer.
If you have an aftermarket seal, they are stiffer than the GM ones, but I don't know if that's enough to cause the hood to lift.

It is the combination of aftermarket seal with worn hood hinges usualy.

-Mark.