for the cylinders at least, if it gets bad you could probably just hone them or something, but usually its just surface rust and theres no harm. if you just keep it all oiled good it shouldn't rust at all really. the block is still fully assembled though? if thats the case, the only thing that youd have to worry too much about is the cylinders. i would rub the cylinders down with oil, put some on the deck, crank it over a few times so its distributed evenly thru the cylinders. flip it over and make sure all the bottom end has oil on it (rods, bottoms of pistons, all the moving parts etc.. now as long as the engine stays assembled you wont have to worry too much about the crank or any of the journals. but no, it would be hard to make enough rust for there to be a problem with the machine shop.