Sure that wasn't the vent tube you saw? Up at the top? There's no vacuum or electrical on the trans. Well, the backup light is electrical, but it's that way on all of the transmissions.
The only Dana 44 that will match the front axle (and be worth swapping) will be one from an MJ/XJ. Or you can swap in an Explorer rear axle. Rubbing is only a problem on them when running stock rims and wide tires.