Hello Chris,
The simple answer is "don't worry" – if you give it a try, I think you will find it perfectly feasible to chamfer the bulkheads the way they are now, i.e. already glued to the keel. It might be a tad easier if the amount of chamfer is established by dryfitting only, while the actual chamfering is carried out with the bulkheads separate; however, it is in no way impossible or even very difficult to do with them in situ.
Use a couple of strips of wood as temporary stringers to check the amount of chamfering needed for each bulkhead, and then file and sand until the stringers can be laid neatly along the edges of all the bulkheads.
For some very useful tips and guides on planking, I can heartilly recommend the articles on this page: **LINK**
Here's wishing you good luck and lots of fun!
Mattias