So its a known good gearbox, good clutch and the gear linkage alignment has been checked. That doesn't leave a lot.
How about the push-rod bearing underneath the end cap of the gearbox, where the lever arm operates. They can break up and cause problems. Much the same as a traditional release bearing.
Without engine running, do the gears engage ok? If not, as rubjonny says, disconnect the linkage and try the selector on the box. If thats ok, then its your linkage. If thats all good, then its pointing towards your clutch or that bearing that I mentioned.
