Some small differences, all machined surfaces, bolt holes, alignment pins are the same. There may be slight clearance issues requiring a little grinding internally on the 394 if using early flywheel and clutch. Most differences are "cosmetic" like the round windows went away with the 371, The 394 had cast buttresses added at the top of the bell.. There are a few other slight differences..
Alignment pins are in the same place, however if the 324 was used with the single coupling hydramatic, the pins were on the block. The later blocks had the pins in the transmission. I know that this is true for 303 with hydramatic. (I mounted the older hydramatic to a 1960 371. The 371 had the dual coupling hydramatic, which had the pins on it.