Engine refitting
 

Ok, the engine is now bolted fully to the gearbox, all barring one bolt fitted (starts motor) all fitted snugly, however the engine mount studs are still about 1cm in front of the holes on the subframe.! Any ideas how I get them to line up?

Had that problem a few times bud, try jacking the gear box up a little and put the engine crane back on the engine and lift it slightly just enough so the mount bolts are just touching the cradle but enough so you can rock the engine, then get a long leaver bar and gently push the stud into place, making sure you don't damage the thread on the mount.