My old trad had the Everflex hood and water came in through the stitch holes. I tried wax but didn’t work. Seam sealer worked much better. Worst leaks were from the front, water getting under from the screen frame. Stick on neoprene section sorted that.
Got a Plus Four now with easy up (?) hood. Not used in rain yet. My first thoughts are is the hood physically sealing down onto the body when the catches engage? Try the Cooperman test. If no catch adjustment cures it then perhaps some thin extra sealing strip might be needed to bridge the gap.
An odd thing but, try pushing the rear down in a different order. It might ( it’s a Morgan after all) mean better setting of the catches if done in reverse order.
