i'm not really understanding your ? or what your looking to do. the lines from the tranny to the rad thread into the cooler, there should be no need to put any sealer on them.
Do you mean you have an AUTOMATIC radiator in a STANDARD transmission car? And you just want to plug the holes? I would just put a bolt or plug in there that fits. Squirting RTV could ruin it for use down the road if you ever decided to use the area as an oil or powersteering cooler.
IIRC it's a 1/4" NPT fitting in the radiator itself (sound right Paul?). The intermediate fittings are what convert NPT to flare type fittings. Remove these fittings from the radiator to expose the NPT fittings.
Lowes has what you should need (you might need a double male 1/4" NPT and then a female 1/4 cap). Do that for each fitting.