Not having much vacuum could certainly be your problem with hard shifting. Since Diesels don't have manifold vacuum, they have a seperate pump to provide vacuum for all the systems. If your power brakes are working, your pump is probably just fine and you just need to check for leaks or make adjustments to get your shifting back in shape.
Unfortunately, vacuum is not my problem. One of the first things I did was disconnect the vacuum modulator to see if I could force it to shift... It didn't help. Most likely I'll have to replace the clutch packs (unless I can find a good used trans).