I would try and get the water flow issue addressed first. If the engine is getting very hot with the restricted flow, it may be the reason your patch is starting to leak. If it's just the patch letting go, then the JB Weld should do the trick.
Take note also if it's the patch letting go or if the block looks like it's starting to have a larger crack which would probably require a larger patching job than JB Weld alone. Check out
http://www.canadascapitalas.com/tech_castiron.asp for details on patching cast.
Did you notice anything different the other Model A drivers did when they ran your car? If the car is idling high (carb setting, or the pedal is sticking in the floor) , you will have a hard time to shift without grinding.
Best of Luck and I hope it's something small and relatively easy to address.