Hopefully, there wasn't much coolant in your crankcase. The two biggest culprits are the headgasket and a cracked head or block. The right stopleak might fix either one. Yes, antifreeze can ruin your bearings, but a small amount won't hurt much, and if you are going to have to build a new engine sooner or later, it won't make that much difference. We had a fire truck with a major crack in the block, they put 4 cans of alumi-seal in it, and ran it for 3 or 4 years before the truck was sold, and it still ran.
As for your tranny, are you saying you have a 3 speed in a 3/4 ton? I thought they all had the SM420, 4 speed granny box. While I don't think they are the same length, your driveshaft should have a slip joint in it that will allow for some adjustment. Is your shaft open the full length, or is the front half closed?
