Soft start for that size of transformer isn't really needed. Just use a zero volt switching SSR (most AC SSR's are), and you shouldn't have any issues.
One thing to note though, is if the SSR fails, it'll likely fail short circuit, so oversize and fuse it to minimise the risk. If you're really concerned, put a mechanical relay in circuit before it, incase anything does happen.

Generally you only fuse the transformer primary side. Any overload on the secondary side should blow the fuse on the primary side. If you oversize the rectifier enough, then any overload on the DC side should also blow the primary side fuse.
Fusing individual drives isn't usually recommended, as if it fails for any reason, then you risk the drive being fried due it having no where to dump power from a moving motor to.

The drain resistor should simply connect across the capacitor terminals. Unless you have some reason to quickly dump power, you don't need to have it switched. The motor drivers themselves will quickly drain the capacitors with power removed.