I've been looking at purchasing a Juno-G as it's a nice synth, has sampling capabilites and is just a great little system for laying down ideas.

It has MIDI outs so I was wondering that if I put them into the Midi ins on my interface, will I be able to assign it to drum samples in Fruity Loops?

Also, will I be able to use VSTs via MIDI with the pitch changer and an expression pedal on the Juno-G?

Running MIDI from your keys to your interface should work without any problems.

If your keyboard has inputs on it you can probably sample into it and use the on board FX but I am not sure if you can run though the keyboard and use the FX in real time...

MIDI is a control data setup. You can change on screen settings using the keyboard but in order to change audio you need to run though an interface or some kind and in some cases, though the keyboard to get those FX.