In regards to the vibration, it could be a few different things.
It could be a warped rotor (for want of a better word). If you didn't replace the rotors, i'd recommend you do so.
you can get standard rotors from Brakes Direct in QLD for a reasonable price. Housemates Bimmer had a similar issues and I just replaced the rotors and the vibration was gone. If it's worse under braking, it'll probably be a rotor issue.
In regards to your calipers, when you rebuilt them, did you grease EVERYTHING with a rubber seal? that includes the ones that go in the piston pots. They need to be properly greased or they won't slide properly and can seize (I've made this mistake before). And the dust boot obviously need to be on to protect from contaminants.
If you had rust on your pistons, I'd probably have replaced them. I wire-wheeled my pistons and they cleaned up nicely the last time I did a caliper rebuild, but haven't come across rust on any of my brakes before.
Brake fluid doesn't cause rust, it's a hydraulic fluid. If there has been any water in the lines at some point that could cause your rust issue. If that is the case, I'm not sure of any way to salvage them, and would probably replace the calipers, etc.
Assuming you did a full fluid flush upon rebuilding the calipers, it may have been some residual rust in there, because that won't get out of the system through the bleed nipples...
tl;dr check your rotors, and possibly replace them. If a caliper is seized, there wasn't enough grease on the piston seals. Rust = bad. Most likely replace the calipers
hope this helps!