No, but the top ends are all interchangable up until the 77 models. The difference is easy to pick: The early type have long 8mm studs coming out of the cases, whereas the later type have short 10mm studs.
The early type sandwiches the barrel between the cases and the head, compared to the later type which bolts the barrel to the cases, and then the head to the barrel.
Gearboxes have four basic types:
1. Early 5-speed (AT1, AG100, etc). One shaft for the gear lever.
2. Late 5-speed (YZ125A, twin shock DT etc). Two linked shafts for the gear lever.
3. Early 6-speed (YZ125C, YZ125X, etc). Two linked shafts for the gear lever.
4. Late 6-speed (YZ125D+ monoshock DT, etc). Back to one shaft.
You can't simply bolt a Type 3 box into a Type 2 motor as lots of bits are different diameters (input shaft, the rods the shift forks run on, etc).