If it's running smooth and able to go down the road, the noise is probably both valves and injectors. If you obtain a stehescope you can hear them alone and find the noise. The timing chain tensioners and the waterpump and supercharger can be noisy too. If you hear a whinning noise as you turn the steering wheel that will be the electric power steering pump. If you hear a rattle noise as you wind up and shift it can be the clutch. Small car not much room, you hear it all.
Charlie Croker ,BRG 03 Cooper S, SCCA Solo, PDX, Time Trials, RoadRally, and Stella,
011 Oxford Grn Countryman S