AM - after you index and put the outside cover back on and try shifting the gears, you probably need to budge the gears by moving the back tire while you move the shift lever.
If you still can't get all the gears then the indexing is the most likely problem. Unless there is some other condition we're not aware of I can't see why you'd need to take the clutch apart. It's a gearbox problem, not a transmission problem.
So if you indexed in 1st gear you
a) ensured that the camplate was in first gear position
b) let the outer quadrant fall all the way down to the floor of the gearbox and then lifted it up just enough to engage the first teeth on the camplate as you pushed on the inner cover
If everything is still assembled I would try shifting again but moving the gears using the rear wheel and then if you get no joy I would pull off the outer and inner cover and try indexing again.
In your next post can you confirm which bush you replaced and whether everything was working ok before you replaced it?