So I origionally thought that it was the fuel pressure regulator that was causing the rough idle, well now its got a real heavy brake pedal and an even rougher idle, I'm guessing the brake booster is at fault for at least part of this?
Pump the brakes with the engine off and start it up, the pedal does go down a little bit, with the engine running theres pleanty of vacuum from the check valve, sound like the brake booster then?

 

yes it does if the brake pedal gets really hard then its the booster

 

Yeah, I'd say the diaphragm on the booster is shot. Do the master cylinder while you're at it.

 

i agree do the master cylinder at the same time consider it preventive maintenance

 

before you do that, verify the vacuum hose from the engine to the brakes isn't leaking, and is still connected. [8D]

 

I agree with Hanr3, check the vacuum hose first. Also plug the vacuum hose, run the engineand see if the idle smooths out.

I'd only replace the master cylinder if it was leaking out the back into the booster and you should be able to see that when you pull the master cylinder forward, before disconnecting the brake lines.