just fired it up 2day for the first time in the car and its running a bit lumpy. It sounded fine when in the bike and ive not got much idea what it could be.

Only thing i can think is that its because ive changed the exhaust and the difference in back pressure is causing the roughness.

Any help would be much appreciated

How long has it been sitting idle? Has it had all its orifices sealed? Did you lubricate the entire top end before it "went to sleep"?
When you say you changed the exhaust, do you mean the design of the system, or just the routing of the pipes? If you merely re-routed the pipes to suit the chassis, then there's no worries there. If, however, you have had a major re-design of the system, then you may have to re-jet the carbs/re-map the injection (is yours carbed or jected?).
I reckon it's just a bit sleepy. One or more of the valves could be stuck open. Rough as it may sound, I would persevere, and try to get the motor warmed up. As long as there aren't any horrible metal or mechanical noises, then you can't really do it any harm.
It should settle down once it's warmed up sufficiently.
Don't blip the throttle a la boy racer style, all that does is cool the engine with each blip, and each fresh charge of petrol washes the oil off the cylinder walls. Just keep it at a nice steady fast idle.
If the engine's been run in (I presume it was a runner out of a wreck), then switch to semi or fully synthetic bike oil, if you haven't already.